Running as unit: rb-build-arm64_9-79172.service ==================================================================================== Fri Jun 6 06:42:07 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_9) on jenkins, called using "codethink04-arm64 codethink03-arm64" as arguments. Fri Jun 6 06:42:07 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-DaFIiwhu" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Jun 6 06:42:07 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Fri Jun 6 06:42:07 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-wiuRSV' Fri Jun 6 06:42:08 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Fri Jun 6 06:42:08 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-RAiVKF' ok, let's check if seqan2 is building anywhere yet… ok, seqan2 is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of seqan2 in unstable on arm64 on jenkins now. 1st build will be done on codethink04-arm64.debian.net. 2nd build will be done on codethink03-arm64.debian.net. ============================================================================= Fri Jun 6 06:42:11 UTC 2025 I: starting to build seqan2/unstable/arm64 on jenkins on '2025-06-06 06:42' Fri Jun 6 06:42:11 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_9/79172/console.log 1749192131 arm64 unstable seqan2 Fri Jun 6 06:42:11 UTC 2025 I: Downloading source for unstable/seqan2=2.4.0+dfsg-16 --2025-06-06 06:42:11-- http://deb.debian.org/debian/pool/main/s/seqan2/seqan2_2.4.0%2bdfsg-16.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2321 (2.3K) [text/prs.lines.tag] Saving to: ‘seqan2_2.4.0+dfsg-16.dsc’ 0K .. 100% 263M=0s 2025-06-06 06:42:11 (263 MB/s) - ‘seqan2_2.4.0+dfsg-16.dsc’ saved [2321/2321] --2025-06-06 06:42:11-- http://deb.debian.org/debian/pool/main/s/seqan2/seqan2_2.4.0%2bdfsg-16.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2321 (2.3K) [text/prs.lines.tag] Saving to: ‘seqan2_2.4.0+dfsg-16.dsc’ 0K .. 100% 263M=0s 2025-06-06 06:42:11 (263 MB/s) - ‘seqan2_2.4.0+dfsg-16.dsc’ saved [2321/2321] Fri Jun 6 06:42:11 UTC 2025 I: seqan2_2.4.0+dfsg-16.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: seqan2 Binary: seqan-apps, libseqan2-dev Architecture: any all Version: 2.4.0+dfsg-16 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Michael R. Crusoe , Kevin Murray Homepage: https://www.seqan.de/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/seqan2 Vcs-Git: https://salsa.debian.org/med-team/seqan2.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@, libbam-dev, libboost-dev, libbz2-dev, zlib1g-dev Build-Depends: debhelper-compat (= 13), python3, cmake, fakeroot Build-Depends-Arch: zlib1g-dev, libbz2-dev, libbam-dev, libboost-dev, help2man, ctdconverter Package-List: libseqan2-dev deb libdevel optional arch=all seqan-apps deb science optional arch=any Checksums-Sha1: 119b812a854d626deb890762ef57e6a1b2ced0ff 84125556 seqan2_2.4.0+dfsg.orig.tar.xz 3332eb598677c1e17b461d0650c5f41f5a7a7678 29844 seqan2_2.4.0+dfsg-16.debian.tar.xz Checksums-Sha256: 9e69ff4130519b9c9bf019df6faaa280f35d9fd0485cfcfe270c525744bbe86e 84125556 seqan2_2.4.0+dfsg.orig.tar.xz 026ab27337183bb4cc1c48445c4fab33e3bd95edda5fa607d47d42c02cd8ec71 29844 seqan2_2.4.0+dfsg-16.debian.tar.xz Files: c0a126276b1b2864cde3a3b00a7516b5 84125556 seqan2_2.4.0+dfsg.orig.tar.xz d79b35eaad1addebae94ea3b53ff9a78 29844 seqan2_2.4.0+dfsg-16.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWlTqERHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEFjg//VTT9QFxF6NhXAzZ/XW9oMica4tmJ25ai jH3c16n8AjlzWzbMoZnnsASKaM4yn78kYeYFVGU9o5ZUiazAYNXyjN4imKfSs+De R2FTt6obsyutC67hzAfuILPhmlrfo+3MGCe3eKw7CHL8ClVT00TPQjdncEtW8ENK B7nU95nK4bbclevEk9elXn9CTrrJaxulyurUCl5FUt5QDkvKGK2nZEPf40FztK8x y+AgJW7PlHd05pEr6TFdblX0eCjFdG2fiO+lUymQVvap95qwAdkMRQnWd/PCG6pP 9U0tCnAEBTOMYtwEyB6JWmklsX3lh5E6Ip4qAcmzAzqXAATtt/8RP3Hrzk83XSyS IChNuFq7VLNpPkLw3H/j7UB1PNGtPUlr5/TtJZHEAqgwdBSVo7TjUxpfmKt6snTp 6RFPYC1UhXycreL0KCTF/1Jkjeb751uQvxonMtvq78GBXeyMO9O+q2jY0H83feZj rhDTCBr8iSmgoPsWTFtnslGE9kq1Zp7B12ldvqHdDG3Wjn5eaCHZnovIqZ8/jbDT rSbQL7nsnVlJV550r66V2yinADV4a2g4Hxb6N3DKaHlIUWgP3qbuY2RudFO3ekJC JB6OFj7p0ZlEGKwNxoReNSXzCVAdj7yKmVMI1uAnZXD9jHzzrXkY7T82OThBuoTM MFK/QJwm13g= =rwQp -----END PGP SIGNATURE----- Fri Jun 6 06:42:11 UTC 2025 I: Checking whether the package is not for us Fri Jun 6 06:42:11 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Fri Jun 6 06:42:11 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Fri Jun 6 06:42:11 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Fri Jun 6 06:42:11 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-awirac' ==================================================================================== Fri Jun 6 06:42:12 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 seqan2 unstable /srv/reproducible-results/rbuild-debian/r-b-build.g2xuQ2g3 2.4.0+dfsg-16" as arguments. Fri Jun 6 06:42:12 UTC 2025 - actually running "reproducible_build.sh" (md5sum 44ec6a3142940d5e9a7ab76543d96029) as "/tmp/jenkins-script-jnGaWFDl" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Jun 6 06:42:12 UTC 2025 I: Downloading source for unstable/seqan2=2.4.0+dfsg-16 Reading package lists... NOTICE: 'seqan2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/seqan2.git Please use: git clone https://salsa.debian.org/med-team/seqan2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 84.2 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main seqan2 2.4.0+dfsg-16 (dsc) [2321 B] Get:2 http://deb.debian.org/debian unstable/main seqan2 2.4.0+dfsg-16 (tar) [84.1 MB] Get:3 http://deb.debian.org/debian unstable/main seqan2 2.4.0+dfsg-16 (diff) [29.8 kB] Fetched 84.2 MB in 2s (42.4 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'seqan2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/seqan2.git Please use: git clone https://salsa.debian.org/med-team/seqan2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 84.2 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main seqan2 2.4.0+dfsg-16 (dsc) [2321 B] Get:2 http://deb.debian.org/debian unstable/main seqan2 2.4.0+dfsg-16 (tar) [84.1 MB] Get:3 http://deb.debian.org/debian unstable/main seqan2 2.4.0+dfsg-16 (diff) [29.8 kB] Fetched 84.2 MB in 2s (42.4 MB/s) Download complete and in download only mode ============================================================================= Building seqan2 in unstable on arm64 on codethink04-arm64 now. Date: Fri Jun 6 07:42:15 BST 2025 Date UTC: Fri Jun 6 06:42:15 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Jun 5 18:42:15 -12 2025 I: pbuilder-time-stamp: 1749192135 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [seqan2_2.4.0+dfsg-16.dsc] I: copying [./seqan2_2.4.0+dfsg.orig.tar.xz] I: copying [./seqan2_2.4.0+dfsg-16.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./seqan2_2.4.0+dfsg-16.dsc: no acceptable signature found dpkg-source: info: extracting seqan2 in seqan2-2.4.0+dfsg dpkg-source: info: unpacking seqan2_2.4.0+dfsg.orig.tar.xz dpkg-source: info: unpacking seqan2_2.4.0+dfsg-16.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling dpkg-source: info: applying skip-seqan-revision dpkg-source: info: applying fix-version_check-test dpkg-source: info: applying skip-some-apps-on-some-archs dpkg-source: info: applying tweak_readmes dpkg-source: info: applying install_fiona_illumina dpkg-source: info: applying ctdVersion.patch dpkg-source: info: applying fix_manpage_formatting.patch dpkg-source: info: applying no-unaligned-access.patch dpkg-source: info: applying ia64_yield dpkg-source: info: applying python3 dpkg-source: info: applying fix_python3_tests I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/995300/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='fc1dfb2a0a5c4f3380a78027dae3a16a' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='995300' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.g2xuQ2g3/pbuilderrc_CUcN --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.g2xuQ2g3/b1 --logfile b1/build.log seqan2_2.4.0+dfsg-16.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/995300/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), python3, cmake, fakeroot, zlib1g-dev, libbz2-dev, libbam-dev, libboost-dev, help2man, ctdconverter dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19964 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on ctdconverter; however: Package ctdconverter is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} ctdconverter{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbam-dev{a} libboost-dev{a} libboost1.83-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgcrypt20{a} libgnutls30t64{a} libgpg-error0{a} libgssapi-krb5-2{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} libxslt1.1{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} procps{a} python3{a} python3-ctdopts{a} python3-lxml{a} python3-minimal{a} python3-ruamel.yaml{a} python3-ruamel.yaml.clib{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpg-error-l10n libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-bs4 python3-cssselect python3-html5lib wget 0 packages upgraded, 86 newly installed, 0 to remove and 0 not upgraded. Need to get 49.3 MB of archives. After unpacking 310 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.4-1 [855 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.1-1 [93.3 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.4-1 [2002 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.4-1 [27.3 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025b-3 [260 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.8-2 [21.3 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.4-1 [1892 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.4-1 [756 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.4-1 [10.2 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.4-1 [28.3 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-8 [63.0 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-8 [873 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.6-2 [2268 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-1 [629 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-3 [323 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1+b1 [24.2 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 41 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-2 [107 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1.1 [71.4 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.14.1-1 [360 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.6-1 [131 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.50.0-2 [148 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.6-2 [9906 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-ctdopts all 1.5-5 [22.5 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libgpg-error0 arm64 1.51-4 [78.5 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libxslt1.1 arm64 1.1.35-1.2 [221 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-lxml arm64 5.4.0-1 [1139 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-ruamel.yaml.clib arm64 0.2.12+ds-1+b1 [117 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 python3-ruamel.yaml all 0.18.10+ds-1 [147 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 ctdconverter all 2.1-8 [27.9 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 75 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libbam-dev arm64 0.1.19+dfsg-6 [110 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-4.2 [10.6 MB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 86 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Fetched 49.3 MB in 0s (141 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19964 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.4-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.4-1) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.4-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.4-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.4-1_arm64.deb ... Unpacking python3.13 (3.13.4-1) ... 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Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-8_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-8) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.4-8_arm64.deb ... Unpacking procps (2:4.0.4-8) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../05-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. 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Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libjsoncpp26:arm64 (1.9.6-3) ... Setting up libproc2-0:arm64 (2:4.0.4-8) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libk5crypto3:arm64 (1.21.3-5) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-9) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:arm64 (1.8.0-1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-8) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... Setting up netbase (6.5) ... Setting up cmake-data (3.31.6-2) ... Setting up librhash1:arm64 (1.4.6-1) ... Setting up libkrb5-3:arm64 (1.21.3-5) ... Setting up libboost-dev:arm64 (1.83.0.2+b2) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... 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Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/seqan2-2.4.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../seqan2_2.4.0+dfsg-16_source.changes dpkg-buildpackage: info: source package seqan2 dpkg-buildpackage: info: source version 2.4.0+dfsg-16 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg' dh_auto_clean find . -type f -name "*.pyc" -delete if [ -d orig ] ; then \ for header in `find orig -name "*generated_forwards.h"` ; do \ mv ${header} `echo $header | sed 's?orig/??'` ; \ done ; \ fi rm -rf orig make[1]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/seqan-apps.substvars debian/libseqan2-dev.substvars debian/files rm -fr -- debian/seqan-apps/ debian/tmp/ debian/libseqan2-dev/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure-arch make[1]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg' # Test seems to fail temporarily (see bug #1058548) find . -name "solution_online_search_finder.cpp*" -delete export DEB_BUILD_ARCH=arm64 ; \ dh_auto_configure --arch -- \ -DSEQAN_STATIC_APPS=False -DSEQAN_NO_DOX=1 \ -DSEQAN_DISABLE_VERSION_CHECK=YES cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DSEQAN_STATIC_APPS=False -DSEQAN_NO_DOX=1 -DSEQAN_DISABLE_VERSION_CHECK=YES .. CMake Warning (dev) at CMakeLists.txt:9 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:16 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Initializing SeqAn Build System... -- Scanning dependencies once in DEVELOP mode... -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Found BZip2: /usr/lib/aarch64-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:359 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:123 (seqan_build_system_init) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/aarch64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") -- Performing Test CXX14_BUILTIN -- Performing Test CXX14_BUILTIN - Success CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:360 (find_package) CMakeLists.txt:123 (seqan_build_system_init) This warning is for project developers. Use -Wno-dev to suppress it. -- Looking for C++ include execinfo.h -- Looking for C++ include execinfo.h - found -- Found Seqan: /build/reproducible-path/seqan2-2.4.0+dfsg/include (found version "2.4.0") -- Selected repository dir: /build/reproducible-path/seqan2-2.4.0+dfsg -- Repository date not determined. -- Repository revision not determined. -- Configuring tests CMake Deprecation Warning at tests/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests CMake Deprecation Warning at tests/align/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/align -- Could NOT find SDE: Intel(R) Software Development Emulator (sde) (missing: SDE_EXECUTABLE SDE_VERSION_STRING) -- Could NOT find Umesimd (missing: UMESIMD_INCLUDE_DIR) -- Performing Test SSE4_SOURCE_RUNS -- Performing Test SSE4_SOURCE_RUNS - Failed -- => Abort simd detection of newer instruction sets -- Performing Test SEQAN_SIMD_SEQANSIMD_SUPPORTED -- Performing Test SEQAN_SIMD_SEQANSIMD_SUPPORTED - Success -- Performing Test SEQANSIMD_AVX512_KNL_SOURCE_RUNS -- Performing Test SEQANSIMD_AVX512_KNL_SOURCE_RUNS - Failed -- Intel Software Development Emulator not found, not building platform emulated tests. -- Intel Software Development Emulator not found, not building platform emulated tests. -- Intel Software Development Emulator not found, not building platform emulated tests. -- Intel Software Development Emulator not found, not building platform emulated tests. CMake Deprecation Warning at tests/align_extend/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/align_extend CMake Deprecation Warning at tests/align_parallel/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/align_parallel -- Could NOT find SDE: Intel(R) Software Development Emulator (sde) (missing: SDE_EXECUTABLE SDE_VERSION_STRING) -- Could NOT find Umesimd (missing: UMESIMD_INCLUDE_DIR) -- Intel Software Development Emulator not found, not building platform emulated tests. -- Intel Software Development Emulator not found, not building platform emulated tests. CMake Deprecation Warning at tests/align_profile/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/align_profile CMake Deprecation Warning at tests/align_split/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/align_split CMake Deprecation Warning at tests/alignment_free/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/alignment_free CMake Deprecation Warning at tests/arg_parse/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/arg_parse CMake Deprecation Warning at tests/bam_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/bam_io CMake Deprecation Warning at tests/basic/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/basic CMake Deprecation Warning at tests/bed_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/bed_io CMake Deprecation Warning at tests/blast/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/blast CMake Deprecation Warning at tests/consensus/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/consensus CMake Deprecation Warning at tests/consensus_v2/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/consensus_v2 CMake Deprecation Warning at tests/find/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/find CMake Deprecation Warning at tests/gff_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/gff_io CMake Deprecation Warning at tests/graph_algorithms/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/graph_algorithms CMake Deprecation Warning at tests/graph_align/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/graph_align CMake Deprecation Warning at tests/graph_msa/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/graph_msa CMake Deprecation Warning at tests/graph_types/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/graph_types CMake Deprecation Warning at tests/index/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/index CMake Deprecation Warning at tests/journaled_set/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/journaled_set CMake Deprecation Warning at tests/journaled_string_tree/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/journaled_string_tree CMake Deprecation Warning at tests/map/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/map CMake Deprecation Warning at tests/misc/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/misc CMake Deprecation Warning at tests/modifier/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/modifier CMake Deprecation Warning at tests/modifier_cyclic_shape/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/modifier_cyclic_shape CMake Deprecation Warning at tests/multiple_translation_units/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/multiple_translation_units CMake Deprecation Warning at tests/parallel/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/parallel CMake Deprecation Warning at tests/parse_lm/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/parse_lm CMake Deprecation Warning at tests/pipe/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/pipe CMake Deprecation Warning at tests/platform/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/platform CMake Deprecation Warning at tests/random/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/random CMake Deprecation Warning at tests/realign/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/realign CMake Deprecation Warning at tests/reduced_aminoacid/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/reduced_aminoacid CMake Deprecation Warning at tests/rna_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/rna_io CMake Deprecation Warning at tests/roi_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/roi_io CMake Deprecation Warning at tests/score/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/score CMake Deprecation Warning at tests/seeds/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/seeds CMake Deprecation Warning at tests/seq_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/seq_io CMake Deprecation Warning at tests/sequence/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/sequence CMake Deprecation Warning at tests/sequence_journaled/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/sequence_journaled CMake Deprecation Warning at tests/simd/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/simd -- Could NOT find SDE: Intel(R) Software Development Emulator (sde) (missing: SDE_EXECUTABLE SDE_VERSION_STRING) -- Could NOT find Umesimd (missing: UMESIMD_INCLUDE_DIR) -- Intel Software Development Emulator not found, not building platform emulated tests. CMake Deprecation Warning at tests/simple_intervals_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/simple_intervals_io CMake Deprecation Warning at tests/statistics/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/statistics CMake Deprecation Warning at tests/store/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/store CMake Deprecation Warning at tests/stream/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/stream CMake Deprecation Warning at tests/swift_local/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/find_swift CMake Deprecation Warning at tests/tabix_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/tabix_io CMake Deprecation Warning at tests/translation/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/translation CMake Deprecation Warning at tests/ucsc_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/test_ucsc_io CMake Deprecation Warning at tests/vcf_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/vcf_io -- Configuring demos CMake Deprecation Warning at demos/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.13.4", minimum required is "2.7") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring apps CMake Deprecation Warning at apps/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at apps/alf/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/alf CMake Deprecation Warning at apps/bs_tools/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/bs_tools CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/bs_tools/CMakeLists.txt:123 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/dfi/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/dfi CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/dfi/CMakeLists.txt:74 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/fiona/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/fiona CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/fiona/CMakeLists.txt:100 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/fx_tools/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/fx_tools CMake Deprecation Warning at apps/gustaf/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/gustaf CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/gustaf/CMakeLists.txt:97 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/insegt/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/insegt CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/insegt/CMakeLists.txt:88 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/mason2/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/mason2 CMake Deprecation Warning at apps/micro_razers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/micro_razers CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/micro_razers/CMakeLists.txt:81 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/ngs_roi/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/ngs_roi CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/ngs_roi/CMakeLists.txt:114 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/pair_align/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/pair_align CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/pair_align/CMakeLists.txt:80 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/param_chooser/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/param_chooser CMake Deprecation Warning at apps/rabema/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/rabema CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/rabema/CMakeLists.txt:110 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/razers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/razers CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/razers/CMakeLists.txt:100 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/razers3/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/razers3 CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/razers3/CMakeLists.txt:127 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/razers3/CMakeLists.txt:128 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/rep_sep/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/rep_sep CMake Deprecation Warning at apps/sak/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/sak CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/sak/CMakeLists.txt:86 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/sam2matrix/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/sam2matrix CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/sam2matrix/CMakeLists.txt:74 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/samcat/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/samcat CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/samcat/CMakeLists.txt:81 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/searchjoin/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/searchjoin CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/searchjoin/CMakeLists.txt:84 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/seqan_tcoffee/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/seqan_tcoffee CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/seqan_tcoffee/CMakeLists.txt:73 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/seqcons2/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/seqcons2 CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/seqcons2/CMakeLists.txt:80 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/sgip/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/sgip CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/sgip/CMakeLists.txt:80 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/snp_store/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/snp_store CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/snp_store/CMakeLists.txt:89 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/splazers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/splazers CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/splazers/CMakeLists.txt:87 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/stellar/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/stellar CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/stellar/CMakeLists.txt:79 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/tree_recon/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/tree_recon CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/tree_recon/CMakeLists.txt:73 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/yara/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/yara CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/yara/CMakeLists.txt:188 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done (9.9s) -- Generating done (0.9s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg' rm -f debian/seqan-apps.debhelper.log debian/rules override_dh_auto_configure-indep make[1]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg' dh_auto_configure --indep -B build -- \ -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY -DSEQAN_NO_DOX=1 cd build && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY -DSEQAN_NO_DOX=1 .. CMake Warning (dev) at CMakeLists.txt:9 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:16 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Initializing SeqAn Build System... -- Selected repository dir: /build/reproducible-path/seqan2-2.4.0+dfsg -- Repository date not determined. -- Repository revision not determined. -- Configuring done (0.6s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/seqan2-2.4.0+dfsg/build make[1]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg' rm -f debian/libseqan2-dev.debhelper.log debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg' dh_auto_build --arch "" cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/seqan2-2.4.0+dfsg -B/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg 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'/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/depend make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/depend [ 0%] Built target seqan_library make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_local.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/DependInfo.cmake "--color=" make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/mason_options.cpp.o make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/depend cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/methylation_levels.cpp.o make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/DependInfo.cmake "--color=" [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/genomic_variants.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/genomic_variants.cpp.o -MF CMakeFiles/mason_sim.dir/genomic_variants.cpp.o.d -o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_454.cpp.o make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/mason_options.cpp.o -MF CMakeFiles/mason_sim.dir/mason_options.cpp.o.d -o CMakeFiles/mason_sim.dir/mason_options.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/external_split_merge.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/methylation_levels.cpp.o -MF CMakeFiles/mason_sim.dir/methylation_levels.cpp.o.d -o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o -MF CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o.d -o CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/external_split_merge.cpp.o -MF CMakeFiles/mason_sim.dir/external_split_merge.cpp.o.d -o CMakeFiles/mason_sim.dir/external_split_merge.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.cpp make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_base.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_454.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_454.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_454.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_base.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_base.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_base.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o -MF CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o.d -o CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:55: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.h:49: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:58, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:41: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:46: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:52: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:53: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.h:53: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:53, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:53, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:45: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(String&, const Graph&, const TPropertyMap&, TValue) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TValue = int; TCargo = GenomicInterval]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1502:18: required from 'void seqan::findIntervals(String&, const IntervalTree&, TValue2) [with TValue = int; TCargo = GenomicInterval; TValue2 = int]' 1502 | findIntervals(result, it.g, it.pm, query); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:718:18: required from here 718 | findIntervals(intervals, svIntervalTree, svPos); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] 1441 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] 1453 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] 1475 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = signed char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = signed char]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:620:16, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const signed char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = signed char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short int; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = signed char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = signed char]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:620:16, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const signed char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = signed char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]', inlined from 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_sam.h:320:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_sam.h:363:43: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_genome.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_genome.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_genome.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:42: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -MF CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o.d -o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:106:14: required from here 106 | if (!open(stream, filename)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:106:14: required from here 106 | if (!open(stream, filename)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:106:14: required from here 106 | if (!open(stream, filename)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:153:56: required from here 153 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:140:13: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:140:13: required from 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:153:56: required from here 153 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:46: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:98:7: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]' 98 | class ModifiedIterator > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:59:25: required from 'void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]' 59 | TFragIter it = begin(frag, seqan::Standard()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:153:26: required from here 153 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:264:56: required from here 264 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:140:13: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 512 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:663:20: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::end(ModifiedString&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]' 663 | TResult tmp(end(host(me), tag_)); | ~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:458:102: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]' 458 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); | ~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:59:25: required from 'void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]' 59 | TFragIter it = begin(frag, seqan::Standard()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:153:26: required from here 153 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:140:13: required from 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:264:56: required from here 264 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:46: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:98:7: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]' 98 | class ModifiedIterator > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:193:25: required from 'void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]' 193 | TFragIter it = begin(frag, seqan::Standard()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:264:26: required from here 264 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 512 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:663:20: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::end(ModifiedString&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]' 663 | TResult tmp(end(host(me), tag_)); | ~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:458:102: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]' 458 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); | ~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:193:25: required from 'void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]' 193 | TFragIter it = begin(frag, seqan::Standard()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:264:26: required from here 264 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:167:18: required from here 167 | if (!open(vcfFileIn, toCString(vcfFileName))) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:40: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:167:18: required from here 167 | if (!open(vcfFileIn, toCString(vcfFileName))) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Built target pair_align_lcs make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/DependInfo.cmake "--color=" /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]', inlined from 'void VcfMaterializer::_appendToVariantsBnd(Variants&, const std::vector&)' at /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:608:69: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In member function 'void VcfMaterializer::_appendToVariantsBnd(Variants&, const std::vector&)': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 0%] Linking CXX static library libmason_sim.a cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/cmake -P CMakeFiles/mason_sim.dir/cmake_clean_target.cmake cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_sim.dir/link.txt --verbose=1 /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /usr/bin/ar qc libmason_sim.a CMakeFiles/mason_sim.dir/external_split_merge.cpp.o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o CMakeFiles/mason_sim.dir/mason_options.cpp.o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o CMakeFiles/mason_sim.dir/simulate_454.cpp.o CMakeFiles/mason_sim.dir/simulate_base.cpp.o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o /usr/bin/ranlib libmason_sim.a make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Built target mason_sim make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Built target pair_align_global_0001 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Built target pair_align_global_1111 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target pair_align_global_0010 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target pair_align_global_0011 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target pair_align_global_1001 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target pair_align_global_1010 make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/param_chooser /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/param_chooser/CMakeFiles/param_chooser.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/param_chooser/CMakeFiles/param_chooser.dir/param_chooser.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/param_chooser && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/param_chooser/CMakeFiles/param_chooser.dir/param_chooser.cpp.o -MF CMakeFiles/param_chooser.dir/param_chooser.cpp.o.d -o CMakeFiles/param_chooser.dir/param_chooser.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:32: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:33, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:39: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:30, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:34: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:676:44: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 676 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:704:47: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 704 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:730:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 730 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:748:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 748 | struct LessSplicedScore : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:770:45: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 770 | struct LessSplicedScoreGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:32: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:36: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h: In instantiation of 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1658:15: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2250:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1430:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 1430 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:222: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1653:13: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1653 | while (find(swiftFinder, swiftPattern, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2242:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2242 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:87: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1653:13: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1653 | while (find(swiftFinder, swiftPattern, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2245:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2245 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1430:19: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]' 1430 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1658:15: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2250:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1431:13: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]' 1431 | TReadRev readRev(readSet[rseqNo]); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1658:15: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2250:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1653:13: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1653 | while (find(swiftFinder, swiftPattern, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2253:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2253 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1653:13: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1653 | while (find(swiftFinder, swiftPattern, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2256:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2256 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 385 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]' 301 | : data_iterator(begin(haystack, Rooted())) | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1399:15: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]' 1399 | TMyersFinder myersFinder(inf); | ^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1658:15: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2250:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:72:7: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]' 72 | class ModifiedIterator | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]' 301 | : data_iterator(begin(haystack, Rooted())) | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1432:19: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]' 1432 | TMyersFinderRev myersFinderRev(infRev); | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1658:15: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2250:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1625:31: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1625 | TReadSet &readSet = host(host(swiftPattern)); | ~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2239:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2239 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]' 278 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1625:31: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1625 | TReadSet &readSet = host(host(swiftPattern)); | ~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2242:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2242 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]' 278 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1625:31: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1625 | TReadSet &readSet = host(host(swiftPattern)); | ~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2245:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2245 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]' 278 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:55, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:28: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1603:45: required from 'bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]' 1603 | TSize haystack_length = length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1636:16: required from 'bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]' 1636 | return find(finder, pattern, state); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1654:16: required from 'bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFindBeginPatternSpec = void]' 1654 | return find(finder, pattern, pattern, minScore); //static cast | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1414:13: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]' 1414 | while (find(myersFinder, myersPattern, minScore)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1658:15: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2250:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 512 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:469:24: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]' 469 | TIterator temp_(end(host(me), Rooted())); | ~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]' 301 | : data_iterator(begin(haystack, Rooted())) | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1432:19: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]' 1432 | TMyersFinderRev myersFinderRev(infRev); | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1658:15: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2250:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:61: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:21: required from 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]' 599 | return container(hostIterator(me)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1603:45: required from 'bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]' 1603 | TSize haystack_length = length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1636:16: required from 'bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]' 1636 | return find(finder, pattern, state); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1654:16: required from 'bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]' 1654 | return find(finder, pattern, pattern, minScore); //static cast | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1437:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2250:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>; typename Reference > >::Type = Segment, Alloc<> >, InfixSegment>&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:840:14: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2047:11: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2047 | setHost(forwardPatterns[i], indexText(swiftIndex)[i]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2239:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2239 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target pair_align_global_1000 make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/param_chooser /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/param_chooser && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -MF CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o.d -o CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp:45: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp:42: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:33, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:30, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:34: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:676:44: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 676 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:704:47: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 704 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:730:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 730 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:748:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 748 | struct LessSplicedScore : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:770:45: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 770 | struct LessSplicedScoreGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:32: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target pair_align_global_1011 make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/rabema/CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o [ 1%] Built target pair_align_global_0111 cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -MF CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o.d -o CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 1%] Building CXX object apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -MF CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o.d -o CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:31: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:27: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:36: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:39: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target pair_align_global_1100 make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema/CMakeFiles/rabema_evaluate.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -MF CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o.d -o CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:42: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:105:10: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 105 | std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:254:100: required from here 254 | TModifiedString rRightInterval(infix(errorCurve, rightmostPos, offset + intervalLength)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:72:7: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]' 72 | class ModifiedIterator | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:257:52: required from here 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]' 512 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:469:24: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]' 469 | TIterator temp_(end(host(me), Rooted())); | ~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:257:52: required from here 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]' 385 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:513:97: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]' 513 | typename Iterator, Tag const >::Type temp_(begin(host(me), Rooted())); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:257:91: required from here 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]', inlined from 'bool seqan::parseGappedParams(RazerSOptions&, TFile&, ParamChooserOptions&) [with TFile = std::__cxx11::basic_stringstream; TSpec = RazerSSpec<>]' at /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:829:51: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::parseGappedParams(RazerSOptions&, TFile&, ParamChooserOptions&) [with TFile = std::__cxx11::basic_stringstream; TSpec = RazerSSpec<>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h: In instantiation of 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); | ~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]' 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 558 | _findBeginInit(pattern, needle); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(Pattern >&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers]' 660 | _patternFirstInit(pattern, needle(pattern)); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 255 | _reinitPattern(me); | ~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from 'void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = long unsigned int]' 403 | Pattern pattern(read, -(int)length(read) * 40); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from 'int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 899 | buildErrorCurvePoints(errorCurves[readId], maxError, contig, record.rID, !hasFlagRC(record), | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 900 | readSeq, readId, endPos, readNameStore, options.matchN, TPatternSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:1203:37: required from here 1203 | res = matchesToErrorFunction(errorCurves, readAlignmentDistances, inBam, readNameStore, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1204 | contigNames(context(inBam)), faiIndex, options, MyersUkkonenReads()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 254 | setValue(_dataHost(me), std::forward(ndl)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from 'void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = long unsigned int]' 403 | Pattern pattern(read, -(int)length(read) * 40); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from 'int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 899 | buildErrorCurvePoints(errorCurves[readId], maxError, contig, record.rID, !hasFlagRC(record), | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 900 | readSeq, readId, endPos, readNameStore, options.matchN, TPatternSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:1203:37: required from here 1203 | res = matchesToErrorFunction(errorCurves, readAlignmentDistances, inBam, readNameStore, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1204 | contigNames(context(inBam)), faiIndex, options, MyersUkkonenReads()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: required from 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]' 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); | ~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]' 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 255 | _reinitPattern(me); | ~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from 'void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = long unsigned int]' 403 | Pattern pattern(read, -(int)length(read) * 40); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from 'int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 899 | buildErrorCurvePoints(errorCurves[readId], maxError, contig, record.rID, !hasFlagRC(record), | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 900 | readSeq, readId, endPos, readNameStore, options.matchN, TPatternSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:1203:37: required from here 1203 | res = matchesToErrorFunction(errorCurves, readAlignmentDistances, inBam, readNameStore, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1204 | contigNames(context(inBam)), faiIndex, options, MyersUkkonenReads()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:29: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:33: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]', inlined from 'bool seqan::parseGappedParams(RazerSOptions&, TFile&, ParamChooserOptions&) [with TFile = std::basic_fstream; TSpec = RazerSSpec<>]' at /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:829:51, inlined from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' at /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1107:20, inlined from 'int main(int, const char**)' at /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'int main(int, const char**)': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target pair_align_global_1101 make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema/CMakeFiles/rabema_do_search.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/rabema/CMakeFiles/rabema_do_search.dir/do_search.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_do_search.dir/do_search.cpp.o -MF CMakeFiles/rabema_do_search.dir/do_search.cpp.o.d -o CMakeFiles/rabema_do_search.dir/do_search.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(String&, const Graph&, const TPropertyMap&, TValue) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TValue = unsigned int; TCargo = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1502:18: required from 'void seqan::findIntervals(String&, const IntervalTree&, TValue2) [with TValue = unsigned int; TCargo = unsigned int; TValue2 = unsigned int]' 1502 | findIntervals(result, it.g, it.pm, query); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:644:22: required from 'int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 644 | findIntervals(queryResult, intervalTrees[seqId], lastPos); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1003:42: required from 'int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 1003 | int res = benchmarkReadResult(result, currentSamRecords, bamFileIn, currentGsiRecords, | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1004 | faiIndex, refSeqs, refIdMapping, options, tagPattern, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1005 | /*pairedEnd=*/ false); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1401:45: required from here 1401 | res = compareAlignedReadsToReference(result, bamFileIn, faiIndex, refSeqs, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1402 | inGsiIter, options, MyersUkkonenReads()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] 1441 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] 1453 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] 1475 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:44, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:3: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:45: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ [ 1%] Linking CXX executable ../../bin/param_chooser cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/param_chooser && /usr/bin/cmake -E cmake_link_script CMakeFiles/param_chooser.dir/link.txt --verbose=1 In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:11: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic -Wl,--dependency-file=CMakeFiles/param_chooser.dir/link.d CMakeFiles/param_chooser.dir/param_chooser.cpp.o -o ../../bin/param_chooser -lrt -lz -lbz2 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h: In instantiation of 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); | ~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]' 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 558 | _findBeginInit(pattern, needle); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(Pattern >&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers]' 660 | _patternFirstInit(pattern, needle(pattern)); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 255 | _reinitPattern(me); | ~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:623:51: required from 'int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 623 | Pattern pattern(readSeq, -static_cast(length(readSeq)) * 1000); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1003:42: required from 'int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 1003 | int res = benchmarkReadResult(result, currentSamRecords, bamFileIn, currentGsiRecords, | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1004 | faiIndex, refSeqs, refIdMapping, options, tagPattern, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1005 | /*pairedEnd=*/ false); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1401:45: required from here 1401 | res = compareAlignedReadsToReference(result, bamFileIn, faiIndex, refSeqs, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1402 | inGsiIter, options, MyersUkkonenReads()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 1%] Built target param_chooser make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers/CMakeFiles/razers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/razers/CMakeFiles/razers.dir/razers.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers/CMakeFiles/razers.dir/razers.cpp.o -MF CMakeFiles/razers.dir/razers.cpp.o.d -o CMakeFiles/razers.dir/razers.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 254 | setValue(_dataHost(me), std::forward(ndl)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:623:51: required from 'int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 623 | Pattern pattern(readSeq, -static_cast(length(readSeq)) * 1000); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1003:42: required from 'int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 1003 | int res = benchmarkReadResult(result, currentSamRecords, bamFileIn, currentGsiRecords, | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1004 | faiIndex, refSeqs, refIdMapping, options, tagPattern, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1005 | /*pairedEnd=*/ false); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1401:45: required from here 1401 | res = compareAlignedReadsToReference(result, bamFileIn, faiIndex, refSeqs, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1402 | inGsiIter, options, MyersUkkonenReads()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: required from 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]' 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); | ~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]' 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 255 | _reinitPattern(me); | ~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:623:51: required from 'int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 623 | Pattern pattern(readSeq, -static_cast(length(readSeq)) * 1000); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1003:42: required from 'int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 1003 | int res = benchmarkReadResult(result, currentSamRecords, bamFileIn, currentGsiRecords, | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1004 | faiIndex, refSeqs, refIdMapping, options, tagPattern, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1005 | /*pairedEnd=*/ false); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1401:45: required from here 1401 | res = compareAlignedReadsToReference(result, bamFileIn, faiIndex, refSeqs, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1402 | inGsiIter, options, MyersUkkonenReads()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:41: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ [ 1%] Linking CXX executable ../../bin/test_funcs_param_chooser cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/param_chooser && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_funcs_param_chooser.dir/link.txt --verbose=1 In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic -Wl,--dependency-file=CMakeFiles/test_funcs_param_chooser.dir/link.d CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -o ../../bin/test_funcs_param_chooser -lrt -lz -lbz2 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target test_funcs_param_chooser make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/depend In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3 /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3 /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3/CMakeFiles/razers3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o -MF CMakeFiles/razers3.dir/razers.cpp.o.d -o CMakeFiles/razers3.dir/razers.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:13: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:105:10: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 105 | std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:43: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:254:100: required from here 254 | TModifiedString rRightInterval(infix(errorCurve, rightmostPos, offset + intervalLength)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:7: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:72:7: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]' 72 | class ModifiedIterator | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:257:52: required from here 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]' 512 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:469:24: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]' 469 | TIterator temp_(end(host(me), Rooted())); | ~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:257:52: required from here 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]' 385 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:513:97: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]' 513 | typename Iterator, Tag const >::Type temp_(begin(host(me), Rooted())); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:257:91: required from here 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h: In instantiation of 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); | ~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]' 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 558 | _findBeginInit(pattern, needle); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(Pattern >&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers]' 660 | _patternFirstInit(pattern, needle(pattern)); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 255 | _reinitPattern(me); | ~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:27:89: required from here 27 | Pattern pattern(read, -static_cast(length(read))); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Built target pair_align_global_1110 make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3 /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3 /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>; typename Reference > >::Type = Segment, Alloc<> >, InfixSegment>&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:840:14: required from 'void seqan::setValue(Holder >&, const TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]' 840 | set(value(me), value_); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 254 | setValue(_dataHost(me), std::forward(ndl)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:27:89: required from here 27 | Pattern pattern(read, -static_cast(length(read))); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: required from 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]' 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); | ~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]' 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 558 | _findBeginInit(pattern, needle); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(Pattern >&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers]' 660 | _patternFirstInit(pattern, needle(pattern)); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 255 | _reinitPattern(me); | ~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:27:89: required from here 27 | Pattern pattern(read, -static_cast(length(read))); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/razers3/CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers3/CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -MF CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o.d -o CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:57: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:41: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:1: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:28, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:29: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:7: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ [ 2%] Linking CXX executable ../../bin/rabema_do_search cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_do_search.dir/link.txt --verbose=1 In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic -Wl,--dependency-file=CMakeFiles/rabema_do_search.dir/link.d CMakeFiles/rabema_do_search.dir/do_search.cpp.o -o ../../bin/rabema_do_search -lrt -lz -lbz2 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Built target rabema_do_search make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3 /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3 /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3/CMakeFiles/razers3_quality2prob.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/razers3/CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers3/CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -MF CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o.d -o CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:41: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:696:44: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 696 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:728:47: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 728 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:760:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 760 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:51: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/outputFormat.h:126:44: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 126 | struct LessGPosRNo : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:1: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]' 996 | if (!open(seqFile, toCString(fileNameList[f]))) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]' 1035 | return loadContigs(store, fileNames, loadSeqs); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]' 1043 | return loadContigs(store, fileNames, true); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:21: required from here 120 | if (!loadContigs(store, toCString(referenceFile))) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]' 996 | if (!open(seqFile, toCString(fileNameList[f]))) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]' 1035 | return loadContigs(store, fileNames, loadSeqs); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]' 1043 | return loadContigs(store, fileNames, true); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:21: required from here 120 | if (!loadContigs(store, toCString(referenceFile))) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]' 996 | if (!open(seqFile, toCString(fileNameList[f]))) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]' 1035 | return loadContigs(store, fileNames, loadSeqs); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]' 1043 | return loadContigs(store, fileNames, true); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:21: required from here 120 | if (!loadContigs(store, toCString(referenceFile))) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]' 996 | if (!open(seqFile, toCString(fileNameList[f]))) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]' 1035 | return loadContigs(store, fileNames, loadSeqs); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]' 1043 | return loadContigs(store, fileNames, true); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:21: required from here 120 | if (!loadContigs(store, toCString(referenceFile))) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:845:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 845 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:862:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 862 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:896:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 896 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:934:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 934 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:968:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 968 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1009:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1009 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1046:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1046 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1087:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1087 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1130:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1130 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1174:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1174 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1218:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1218 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]' 996 | if (!open(seqFile, toCString(fileNameList[f]))) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]' 1035 | return loadContigs(store, fileNames, loadSeqs); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]' 1043 | return loadContigs(store, fileNames, true); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:21: required from here 120 | if (!loadContigs(store, toCString(referenceFile))) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = signed char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = signed char]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:620:16, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const signed char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = signed char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short int; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = signed char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = signed char]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:620:16, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const signed char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = signed char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:127:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]', inlined from 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_sam.h:320:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_sam.h:363:43: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:55: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:221:47: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 221 | struct LessPairErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:6: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:83: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:265:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 265 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:321:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 321 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:366:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 366 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:41: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:622:23: required from here 622 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:622:23: required from here 622 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:7: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:23: required from here 785 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:97: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1348:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1348 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1348:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1348 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1348:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1348 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1351:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1351 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:622:23: required from here 622 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1351:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1351 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1351:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1351 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1356:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1356 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1356:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1356 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1356:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1356 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1359:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1359 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1359:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1359 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1359:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1359 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1362:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1362 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h: In instantiation of 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:492:40: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 492 | if (matchVerify( | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) | ~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1471:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 1471 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1362:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1362 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h: In instantiation of 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1717:15: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]' 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2043:19: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1471:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 1471 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1362:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1362 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:23: required from here 785 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:622:23: required from here 622 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:23: required from here 785 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment, Alloc<> >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 515 | return begin(cont, Rooted()); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter >, StreamIterator > >; TContainer = Segment, Alloc<> >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = SimpleType]' 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const Segment&) [with TStream = VirtualStream >; THost = const String, Alloc<> >; TSpec = InfixSegment]' 789 | write(it, source); | ~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/outputFormat.h:722:12: required from 'void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 722 | file << reads[(*it).rseqNo]; | ~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:232:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 232 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, stats, readNames, readFileNames[0], errorPrbFileName, options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:23: required from here 785 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:622:23: required from here 622 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 385 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:395:32: required from 'seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]' 395 | data_iterator(begin(haystack, Rooted())), haystackEnd(), _needReinit(true), curHit(), endHit(), | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:394:16: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 394 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); | ^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1928:77: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]' 1928 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:222: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2268:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:87: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1699:13: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]' 1699 | while (find(swiftFinder, swiftPattern, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2043:19: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2268:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2271:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1699:13: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]' 1699 | while (find(swiftFinder, swiftPattern, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2043:19: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2271:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1928:77: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]' 1928 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1471:19: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]' 1471 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:492:40: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 492 | if (matchVerify( | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) | ~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1472:13: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]' 1472 | TReadRev readRev(readSet[rseqNo]); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:492:40: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 492 | if (matchVerify( | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) | ~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2279:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2279 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1699:13: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]' 1699 | while (find(swiftFinder, swiftPattern, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2043:19: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2279:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2279 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2282:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2282 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1699:13: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]' 1699 | while (find(swiftFinder, swiftPattern, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2043:19: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2282:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2282 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::QualityExtractor >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:745:69: required from 'void seqan::write(TTarget&, FragmentStore&, Amos) [with TTarget = VirtualStream >; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; Amos = const Tag]' 745 | ModifiedString > quals(fragStore.readSeqStore[idCount]); | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1222:14: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1222 | write(file, store, Amos()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1866:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 1866 | finder.endPos = length(host(finder)); | ~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1934:34: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]' 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1876:41: required from 'bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 1876 | finder.haystackEnd = begin(tmpHost) + (finder.endPos - length(pattern.shape) + 1); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1934:34: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]' 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1845:48: required from 'bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 1845 | hostIterator(finder) = begin(host(finder)) + finder.startPos; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1965:37: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]' 1965 | if (!_nextNonRepeatRange(finder, pattern)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:23: required from here 785 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1866:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 1866 | finder.endPos = length(host(finder)); | ~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1934:34: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]' 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:72:7: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]' 72 | class ModifiedIterator | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]' 301 | : data_iterator(begin(haystack, Rooted())) | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1473:19: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]' 1473 | TMyersFinderRev myersFinderRev(infRev); | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:492:40: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 492 | if (matchVerify( | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) | ~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | : data_container(_toPointer(container_)), | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]' 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment, Alloc<> >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 515 | return begin(cont, Rooted()); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter >, StreamIterator > >; TContainer = Segment, Alloc<> >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = SimpleType]' 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const Segment&) [with TStream = VirtualStream >; THost = const String, Alloc<> >; TSpec = InfixSegment]' 789 | write(it, source); | ~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/outputFormat.h:722:12: required from 'void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 722 | file << reads[(*it).rseqNo]; | ~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:232:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 232 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, stats, readNames, readFileNames[0], errorPrbFileName, options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1662:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:87: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:375:32: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 375 | TReadSet &readSetL = host(host(swiftPatternL)); | ~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]' 278 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1666:31: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]' 1666 | TReadSet &readSet = host(host(swiftPattern)); | ~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2043:19: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' 143 | Index(Index const &other): | ^~~~~ [ 2%] Linking CXX executable ../../bin/rabema_prepare_sam cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_prepare_sam.dir/link.txt --verbose=1 /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:375:32: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 375 | TReadSet &readSetL = host(host(swiftPatternL)); | ~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2268:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]' 278 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1666:31: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]' 1666 | TReadSet &readSet = host(host(swiftPattern)); | ~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2043:19: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2268:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:375:32: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 375 | TReadSet &readSetL = host(host(swiftPatternL)); | ~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2271:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]' 278 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1666:31: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]' 1666 | TReadSet &readSet = host(host(swiftPattern)); | ~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2043:19: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2271:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1603:45: required from 'bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]' 1603 | TSize haystack_length = length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1636:16: required from 'bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]' 1636 | return find(finder, pattern, state); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1654:16: required from 'bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; TFindBeginPatternSpec = void]' 1654 | return find(finder, pattern, pattern, minScore); //static cast | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1455:13: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]' 1455 | while (find(myersFinder, myersPattern, minScore)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:492:40: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 492 | if (matchVerify( | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) | ~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 512 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:469:24: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]' 469 | TIterator temp_(end(host(me), Rooted())); | ~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]' 301 | : data_iterator(begin(haystack, Rooted())) | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1473:19: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]' 1473 | TMyersFinderRev myersFinderRev(infRev); | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:492:40: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 492 | if (matchVerify( | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) | ~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1662:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:845:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 845 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:862:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 862 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:896:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 896 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:934:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 934 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:968:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 968 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1009:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1009 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1046:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1046 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1087:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1087 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1130:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1130 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1174:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1174 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1218:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1218 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic -Wl,--dependency-file=CMakeFiles/rabema_prepare_sam.dir/link.d CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -o ../../bin/rabema_prepare_sam -lrt -lz -lbz2 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1662:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ [ 2%] Built target rabema_prepare_sam make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/depend /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rep_sep /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rep_sep/CMakeFiles/rep_sep.dir/DependInfo.cmake "--color=" /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/build /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rep_sep && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.1.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o -MF CMakeFiles/rep_sep.dir/rep_sep.cpp.o.d -o CMakeFiles/rep_sep.dir/rep_sep.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1662:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:369:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]' 369 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1845:33: required from 'bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 1845 | hostIterator(finder) = begin(host(finder)) + finder.startPos; | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1965:37: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]' 1965 | if (!_nextNonRepeatRange(finder, pattern)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:61: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:21: required from 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]' 599 | return container(hostIterator(me)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1603:45: required from 'bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]' 1603 | TSize haystack_length = length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1636:16: required from 'bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]' 1636 | return find(finder, pattern, state); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1654:16: required from 'bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]' 1654 | return find(finder, pattern, pattern, minScore); //static cast | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1478:13: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]' 1478 | while (find(myersFinderRev, myersPatternRev, maxScore)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:492:40: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 492 | if (matchVerify( | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) | ~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_shortcuts.h:340:12: required from 'typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = Segment, Alloc<> >, InfixSegment>; typename ReverseComplementString::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]' 340 | return TRevComp(host); | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:936:80: required from 'void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]' 936 | _fillBamSeqAndQual(record.seq, record.qual, reverseComplementString(store.readSeqStore[alignedRead.readId])); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:140:13: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter >, StreamIterator > >; TSequence = Segment, Alloc<> >, InfixSegment>; TSize = int]' 489 | TIter iter = begin(seq, Rooted()); | ~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:740:27: required from 'void seqan::write(TTarget&, FragmentStore&, Amos) [with TTarget = VirtualStream >; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; Amos = const Tag]' 740 | writeWrappedString(iter, fragStore.readSeqStore[idCount], 60); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1222:14: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1222 | write(file, store, Amos()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:98:7: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::begin(const ModifiedString&, Tag) [with THost = const Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]' 98 | class ModifiedIterator > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter >, StreamIterator > >; TSequence = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TSize = int]' 489 | TIter iter = begin(seq, Rooted()); | ~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:746:27: required from 'void seqan::write(TTarget&, FragmentStore&, Amos) [with TTarget = VirtualStream >; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; Amos = const Tag]' 746 | writeWrappedString(iter, quals, 60); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1222:14: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1222 | write(file, store, Amos()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 254 | setValue(_dataHost(me), std::forward(ndl)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1971:11: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 1971 | setHost(forwardPatterns[i], indexText(swiftIndex)[i]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]' 887 | create(me, value_); | ~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 135 | assignValue(*this, value_); | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_wotd.h:259:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:394:16: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 394 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); | ^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:14: required from here 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3247:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:223: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2785:21: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]' 2785 | _patternInit(filterPattern, options.errorRate); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1088:24: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1088 | _applyFilterOptions(filterPatternL, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:14: required from here 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:222: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2896:17: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]' 2896 | _patternInit(filterPattern, options.errorRate, 0); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1088:24: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1088 | _applyFilterOptions(filterPatternL, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3247:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3247:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = Hamming_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2785:21: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = Hamming_; TOptions = RazerSCoreOptions >]' 2785 | _patternInit(filterPattern, options.errorRate); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1088:24: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1088 | _applyFilterOptions(filterPatternL, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:14: required from here 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2896:17: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]' 2896 | _patternInit(filterPattern, options.errorRate, 0); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1088:24: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1088 | _applyFilterOptions(filterPatternL, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3247:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = signed char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = signed char]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:620:16, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const signed char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = signed char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short int; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = signed char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = signed char]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:620:16, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const signed char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = signed char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:14: required from here 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3247:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3247:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:14: required from here 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]', inlined from 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_sam.h:320:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_sam.h:363:43: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:55, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:32: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:969:48: required from 'bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]' 969 | pattern.finderLength = length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2979:24: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3216:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2785:21: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]' 2785 | _patternInit(filterPattern, options.errorRate); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3026:24: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 3026 | _applyFilterOptions(filterPattern, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3221:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2979:24: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3221:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:2081:73: required from 'bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 2081 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1200:29: required from 'void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1489:38: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:296:20: required from 'void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >; TShape = Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]' 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:751:33: required from 'void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 751 | workVerification(tls, job, splitters); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1033:44: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2785:21: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]' 2785 | _patternInit(filterPattern, options.errorRate); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:872:28: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]' 872 | _applyFilterOptions(filterPattern, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:296:20: required from 'void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]' 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:751:33: required from 'void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 751 | workVerification(tls, job, splitters); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1033:44: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2896:17: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]' 2896 | _patternInit(filterPattern, options.errorRate, 0); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3026:24: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 3026 | _applyFilterOptions(filterPattern, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3216:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2979:24: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3216:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2896:17: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]' 2896 | _patternInit(filterPattern, options.errorRate, 0); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:872:28: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]' 872 | _applyFilterOptions(filterPattern, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:296:20: required from 'void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]' 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:751:33: required from 'void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 751 | workVerification(tls, job, splitters); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1033:44: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:969:48: required from 'bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]' 969 | pattern.finderLength = length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = Hamming_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2785:21: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = Hamming_; TOptions = RazerSCoreOptions >]' 2785 | _patternInit(filterPattern, options.errorRate); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3026:24: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 3026 | _applyFilterOptions(filterPattern, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3221:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:2081:73: required from 'bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 2081 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1200:29: required from 'void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1489:38: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = Hamming_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2785:21: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = Hamming_; TOptions = RazerSCoreOptions >]' 2785 | _patternInit(filterPattern, options.errorRate); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:872:28: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]' 872 | _applyFilterOptions(filterPattern, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2896:17: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]' 2896 | _patternInit(filterPattern, options.errorRate, 0); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3026:24: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 3026 | _applyFilterOptions(filterPattern, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3216:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2896:17: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]' 2896 | _patternInit(filterPattern, options.errorRate, 0); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:872:28: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]' 872 | _applyFilterOptions(filterPattern, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2979:24: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3216:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2979:24: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3221:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:296:20: required from 'void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >; TShape = Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]' 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:751:33: required from 'void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 751 | workVerification(tls, job, splitters); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1033:44: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:296:20: required from 'void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]' 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:751:33: required from 'void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 751 | workVerification(tls, job, splitters); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1033:44: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2979:24: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3216:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:296:20: required from 'void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]' 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:751:33: required from 'void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 751 | workVerification(tls, job, splitters); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1033:44: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:22: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:90: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]' 679 | return begin(me, Tag()) + pos; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]' 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = String, Alloc<> >; TGapAnchors = String, Alloc<> >; TPosition = long int; TCount = unsigned int]' 466 | TIter it = iter(gaps, clippedViewPos); | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_base.h:513:15: required from 'void seqan::insertGap(Gaps&, TPosition) [with TSequence = String, Alloc<> >; TSpec = AnchorGaps, Alloc<> > >; TPosition = long int]' 513 | insertGaps(gaps, clippedViewPos, 1u); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2067:42: required from 'void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TScore = Score >; TShrinkMatches = True]' 2067 | insertGap(gaps, insPos - rBegin); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1221:40: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1221 | convertMatchesToGlobalAlignment(store, scoreType, True()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)' is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)' is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 385 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:395:32: required from 'seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]' 395 | data_iterator(begin(haystack, Rooted())), haystackEnd(), _needReinit(true), curHit(), endHit(), | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:680:20: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 680 | TFilterFinderR filterFinderR(genomeInf, options.repeatLength, 1); | ^~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3247:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:932:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]' 932 | finder.endPos = length(host(finder)); | ~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:975:34: required from 'bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]' 975 | if (!_firstNonRepeatRange(finder, pattern)) return false; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:941:46: required from 'bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]' 941 | finder.haystackEnd = begin(host(finder)) + (finder.endPos - length(pattern.shape) + 1); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:975:34: required from 'bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]' 975 | if (!_firstNonRepeatRange(finder, pattern)) return false; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1866:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 1866 | finder.endPos = length(host(finder)); | ~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:2088:30: required from 'bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 2088 | if (!_firstNonRepeatRange(finder, pattern)) return false; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1200:29: required from 'void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1489:38: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:932:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]' 932 | finder.endPos = length(host(finder)); | ~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:975:34: required from 'bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]' 975 | if (!_firstNonRepeatRange(finder, pattern)) return false; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1866:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 1866 | finder.endPos = length(host(finder)); | ~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:2088:30: required from 'bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 2088 | if (!_firstNonRepeatRange(finder, pattern)) return false; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1200:29: required from 'void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1489:38: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]' 250 | return value(me); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:24: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >]' 209 | if ((TVal1)*it1 == (TVal2)*it2) | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement, Alloc<> >, GapAnchor, void>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 529 | _alignAndGetCigarString(cigar, md, contigInfix, readSeq, alignedRead, errors, functor); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]' 905 | alignAndGetCigarString(record.cigar, record.qual, store.contigStore[alignedRead.contigId], | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | store.readSeqStore[alignedRead.readId], alignedRead, errors, functor); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]' 250 | return value(me); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >]' 209 | if ((TVal1)*it1 == (TVal2)*it2) | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement, Alloc<> >, GapAnchor, void>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 529 | _alignAndGetCigarString(cigar, md, contigInfix, readSeq, alignedRead, errors, functor); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]' 905 | alignAndGetCigarString(record.cigar, record.qual, store.contigStore[alignedRead.contigId], | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | store.readSeqStore[alignedRead.readId], alignedRead, errors, functor); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >, GapsIterator > > > > > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >, GapsIterator > > > > > >]' 250 | return value(me); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >]' 209 | if ((TVal1)*it1 == (TVal2)*it2) | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:534:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement, Alloc<> >, GapAnchor, void>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 534 | _alignAndGetCigarString(cigar, md, contigInfix, reverseComplementString(readSeq), alignedRead, errors, functor); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]' 905 | alignAndGetCigarString(record.cigar, record.qual, store.contigStore[alignedRead.contigId], | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | store.readSeqStore[alignedRead.readId], alignedRead, errors, functor); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 520 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:663:20: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::end(ModifiedString&, Tag) [with THost = const Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]' 663 | TResult tmp(end(host(me), tag_)); | ~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:458:102: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]' 458 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); | ~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:811:66: required from 'void seqan::_fillBamSeqAndQual(TSeq&, TQual&, const TRead&) [with TSeq = String, Alloc<> >; TQual = String >; TRead = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]' 811 | typename Iterator::Type sIt = begin(read, Standard()); | ~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:936:31: required from 'void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]' 936 | _fillBamSeqAndQual(record.seq, record.qual, reverseComplementString(store.readSeqStore[alignedRead.readId])); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]' 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]' 174 | appendValue(me.strings, obj, tag); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]' 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:398:24: required from 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >]' 398 | appendValue(indexText(indexL), readSetL[j]); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = const Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]' 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = const Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]' 174 | appendValue(me.strings, obj, tag); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]' 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:859:24: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >]' 859 | appendValue(indexText(index), store.readSeqStore[j]); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]' 205 | return TProxy(it); | ^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]' 250 | return value(me); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:24: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >]' 209 | if ((TVal1)*it1 == (TVal2)*it2) | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]' 205 | return TProxy(it); | ^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]' 250 | return value(me); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >]' 209 | if ((TVal1)*it1 == (TVal2)*it2) | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >, GapsIterator > > > > > >]' 205 | return TProxy(it); | ^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >, GapsIterator > > > > > >]' 250 | return value(me); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >]' 209 | if ((TVal1)*it1 == (TVal2)*it2) | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:534:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:654:36: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 654 | TReadSet & readSetL = host(host(filterPatternL)); | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 512 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:469:24: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]' 469 | TIterator temp_(end(host(me), Rooted())); | ~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]' 301 | : data_iterator(begin(haystack, Rooted())) | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2241:41: required from 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]' 2241 | TMyersFinderRev myersFinderRev(infRev); | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Pigeonhole; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2795:64: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]' 2795 | std::cout << " stepsize: " << getStepSize(host(filterPattern)) << std::endl; | ~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1088:24: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:852:30: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >]' 852 | TIndex & index = host(tls.filterPattern); | ~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Pigeonhole; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:852:30: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]' 852 | TIndex & index = host(tls.filterPattern); | ~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:654:36: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 654 | TReadSet & readSetL = host(host(filterPatternL)); | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:852:30: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]' 852 | TIndex & index = host(tls.filterPattern); | ~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:29: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:989:66: required from 'bool seqan::_patternInitSmallStateBanded(TFinder&, const TNeedle2&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = const Segment, Alloc<> >, InfixSegment>; TNeedle2 = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]' 989 | typename Size::Type const columns = length(container(finder)) + state.leftClip; | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1181:44: required from 'bool seqan::_stateInit(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = const Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]' 1181 | return _patternInitSmallStateBanded(finder, needle, state); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1535:24: required from 'bool seqan::find(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = const Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]' 1535 | if (!_stateInit(finder, needle, state)) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1646:16: required from 'bool seqan::find(TFinder&, const TNeedle&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = const Segment, Alloc<> >, InfixSegment>; TSpec = AlignTextBanded; TFindBeginPatternSpec = void]' 1646 | return find(finder, needle, state); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2177:16: required from 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]' 2177 | while (find(myersFinder, readPrefix, state, minScore)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:61: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_interface.h:430:24: required from 'void seqan::goEnd(TIterator&) [with TIterator = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]' 430 | goEnd(it, container(it)); | ~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:737:10: required from 'void seqan::goEnd(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void]' 737 | goEnd(hostIterator(me)); | ~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1537:18: required from 'bool seqan::find(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]' 1537 | goEnd(finder); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1646:16: required from 'bool seqan::find(TFinder&, const TNeedle&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = AlignTextBanded; TFindBeginPatternSpec = void]' 1646 | return find(finder, needle, state); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2245:32: required from 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]' 2245 | while (find(myersFinderRev, readRev, verifier.revPatternState, maxScore)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2948:40: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 2948 | TReadSet & readSet = indexText(host(filterPattern)); | ~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Pigeonhole; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2795:64: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]' 2795 | std::cout << " stepsize: " << getStepSize(host(filterPattern)) << std::endl; | ~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3026:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:41: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]' 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]' 174 | appendValue(me.strings, obj, tag); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]' 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:398:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]' 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]' 174 | appendValue(me.strings, obj, tag); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]' 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:398:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Pigeonhole >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)' first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = const Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = const Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]' 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = const Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]' 174 | appendValue(me.strings, obj, tag); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]' 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:859:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = const Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = const Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]' 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = const Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]' 174 | appendValue(me.strings, obj, tag); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]' 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:859:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 251 | limitRead(value(filter.callback), readId, newLimit - 1); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 466 | disabled += processRead(*tls.matchFilter, it->readId); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)' first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2948:40: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 2948 | TReadSet & readSet = indexText(host(filterPattern)); | ~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Swift > > >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)' first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 251 | limitRead(value(filter.callback), readId, newLimit - 1); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 466 | disabled += processRead(*tls.matchFilter, it->readId); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)' first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Pigeonhole >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)' first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 251 | limitRead(value(filter.callback), readId, newLimit - 1); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 466 | disabled += processRead(*tls.matchFilter, it->readId); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)' first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Swift > > >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)' first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 251 | limitRead(value(filter.callback), readId, newLimit - 1); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 466 | disabled += processRead(*tls.matchFilter, it->readId); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)' first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Pigeonhole >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 251 | limitRead(value(filter.callback), readId, newLimit - 1); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 466 | disabled += processRead(*tls.matchFilter, it->readId); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Swift > > >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 251 | limitRead(value(filter.callback), readId, newLimit - 1); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 466 | disabled += processRead(*tls.matchFilter, it->readId); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Pigeonhole >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 251 | limitRead(value(filter.callback), readId, newLimit - 1); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 466 | disabled += processRead(*tls.matchFilter, it->readId); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Swift > > >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 251 | limitRead(value(filter.callback), readId, newLimit - 1); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 466 | disabled += processRead(*tls.matchFilter, it->readId); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]' 887 | create(me, value_); | ~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 135 | assignValue(*this, value_); | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:175:9: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:56: required from 'typename seqan::Source > > >::Type seqan::source(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 169 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 193 | else return *source(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const Proxy >&) [with TIterator = Iter, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > >; typename GetValue > >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 275 | return getValue(iter(me)); | ~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_base.h:151:37: required from 'typename seqan::Convert >::Type seqan::convertImpl(Convert, const Proxy&) [with TTarget = char; T = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; TSpec = IteratorProxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > >; typename Convert >::Type = char]' 151 | return convert(getValue(source)); | ~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_conversion.h:149:23: required from 'typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = char; TSource = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; typename Convert::Type = char]' 149 | return convertImpl(Convert(), source); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:241:45: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]' 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: required from 'TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]' 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag; TIntegral = long int]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:634:69: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]' 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: required from 'TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]' 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:46: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) | ~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]' 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: required from 'TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]' 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:744:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 744 | TConstSeqHIterator seqHIter = seqHIterBegin; | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]' 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: required from 'TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]' 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:56: required from 'typename seqan::Source > > >::Type seqan::source(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 169 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 193 | else return *source(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const Proxy >&) [with TIterator = Iter, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > >; typename GetValue > >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 275 | return getValue(iter(me)); | ~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_alphabet_expansion.h:357:37: required from 'typename seqan::Convert >, seqan::Proxy >::Type seqan::convertImpl(Convert >, T>, const Proxy&) [with THost = SimpleType; char CHAR = '-'; TSpec = Tag; T = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; TSpec2 = IteratorProxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > >; typename Convert >, Proxy >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 357 | return convert(getValue(source_)); | ~~~~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_conversion.h:149:23: required from 'typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = ModifiedAlphabet, ModExpand<'-'> >; TSource = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; typename Convert::Type = ModifiedAlphabet, ModExpand<'-'> >]' 149 | return convertImpl(Convert(), source); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_alphabet_expansion.h:92:59: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 385 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:17: required from 'typename seqan::Source > > >::Type seqan::source(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 169 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 193 | else return *source(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const Proxy >&) [with TIterator = Iter, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > >; typename GetValue > >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 275 | return getValue(iter(me)); | ~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_base.h:151:37: required from 'typename seqan::Convert >::Type seqan::convertImpl(Convert, const Proxy&) [with TTarget = char; T = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; TSpec = IteratorProxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > >; typename Convert >::Type = char]' 151 | return convert(getValue(source)); | ~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_conversion.h:149:23: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:994:55: required from 'void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag]' 994 | TConstSeqVIterator itVEnd = begin(seqV, Rooted()) + _min(seqVlength - 1, lowerDiagonal(band) + seqHlength); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:612:32: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 612 | _computeHammingDistance(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoringScheme, band, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 613 | dpProfile); | ~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]' 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:45: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]' 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 520 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:29: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) | ~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]' 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(const ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = ModView > >; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:314:32: required from 'typename seqan::Position > >::Type seqan::position(const ModifiedIterator >&) [with THost = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >; typename Position > >::Type = long unsigned int]' 314 | return length(container(host(me))); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:675:73: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 675 | sequenceEntryForScore(scoringScheme, seqV, position(seqVBegin)), scoringScheme, | ~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]' 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:288:16: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 288 | TContainer cont(container(host(me))); | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 2%] Linking CXX executable ../../bin/rabema_build_gold_standard cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_build_gold_standard.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic -Wl,--dependency-file=CMakeFiles/rabema_build_gold_standard.dir/link.d CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -o ../../bin/rabema_build_gold_standard -lrt -lz -lbz2 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Built target rabema_build_gold_standard make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/sak /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/sak/CMakeFiles/sak.dir/sak.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/sak && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.4.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/sak/CMakeFiles/sak.dir/sak.cpp.o -MF CMakeFiles/sak.dir/sak.cpp.o.d -o CMakeFiles/sak.dir/sak.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | : data_container(_toPointer(container_)), | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: required from 'seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]' 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:56: required from 'typename seqan::Source > > >::Type seqan::source(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 169 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 193 | else return *source(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const Proxy >&) [with TIterator = Iter, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > >; typename GetValue > >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 275 | return getValue(iter(me)); | ~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_base.h:151:37: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = ModView > >; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:30: required from 'typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]' 278 | TContainer cont(container(host(me))); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:397:81: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSeqHValue = SimpleType; TSeqVValue = SimpleType; TSeqVIterator = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >; TScoringScheme = Score >; TDPCell = DPCell_ >; TColumnDescriptor = MetaColumnDescriptor, Tag >; TDPProfile = DPProfile_ >, Tag, TracebackOn, Tag > >, Tag >]' 397 | tmpSeqH, sequenceEntryForScore(scoringScheme, container(iter), position(iter)), | ~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:891:38: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 891 | _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 892 | sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 893 | sequenceEntryForScore(scoringScheme, seqV, 0), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 894 | seqVBegin, seqVEnd, scoringScheme, cacheDiag, cacheVert, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 895 | MetaColumnDescriptor(), dpProfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; TSource = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:702:11: required from 'void seqan::assignValue(T&, TPos, const TValue&) [with T = String, AlignedReadStoreElement, void>, long unsigned int>, Alloc<> >; TValue = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; TPos = unsigned int]' 702 | assign(value(me, pos), _value); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_types/property_map_generic.h:186:16: required from 'typename seqan::EnableIf >, void>::Type seqan::assignProperty(TPropertyMap&, TDescriptor, TValue) [with TPropertyMap = String, AlignedReadStoreElement, void>, long unsigned int>, Alloc<> >; TDescriptor = unsigned int; TValue = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; typename EnableIf >, void>::Type = void]' 186 | assignValue(pm, _getId(d), val); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph_base.h:191:23: required from 'GraphCargo& registerRead(ReadGraph&, typename ReadGraph::TId) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int; typename ReadGraph::TId = unsigned int]' 191 | assignProperty(me.vertexCargo, vd, new_cargo); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph_construction.h:82:59: required from 'void construct(ReadGraph&, const seqan::String > >&, const seqan::FragmentStore&, TId) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int; TSpec = void; TConfig = seqan::FragmentStoreConfig; TId = int]' 82 | TGraphCargo & new_cargo = registerRead(me, _readId(value(colIter))); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:217:14: required from here 217 | construct(rgraph, candidates, fragStore, options.contig); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>& GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>::operator=(const GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>&)' is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph.h:32, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:34: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph_base.h:44:5: note: because 'GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>' has user-provided 'GraphCargo::GraphCargo(const GraphCargo&) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int]' 44 | GraphCargo(GraphCargo const& other) | ^~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 889 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 924 | assignValue(target_, value(source_)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' 150 | assign(*this, source_); | ~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]' 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 889 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 924 | assignValue(target_, value(source_)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' 150 | assign(*this, source_); | ~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]' 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 889 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 924 | assignValue(target_, value(source_)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' 150 | assign(*this, source_); | ~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]' 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 889 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 924 | assignValue(target_, value(source_)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' 150 | assign(*this, source_); | ~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]' 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 889 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 924 | assignValue(target_, value(source_)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' 150 | assign(*this, source_); | ~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]' 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 889 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 924 | assignValue(target_, value(source_)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' 150 | assign(*this, source_); | ~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]' 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Built target pair_align_global_0100 make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/sam2matrix /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/sam2matrix/CMakeFiles/sam2matrix.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/sam2matrix && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -MF CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o.d -o CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:46: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = signed char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = signed char]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:620:16, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const signed char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = signed char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short int; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = signed char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = signed char]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:620:16, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const signed char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = signed char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]', inlined from 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_sam.h:320:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_sam.h:363:43: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:46: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:337:23: required from here 337 | openRes = open(inFile, toCString(options.inFastxPath)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:337:23: required from here 337 | openRes = open(inFile, toCString(options.inFastxPath)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:337:23: required from here 337 | openRes = open(inFile, toCString(options.inFastxPath)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:347:23: required from here 347 | openRes = open(outFile, toCString(options.outPath)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:337:23: required from here 337 | openRes = open(inFile, toCString(options.inFastxPath)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TSequence = Segment, Alloc<> >, InfixSegment>; TSize = int]' 489 | TIter iter = begin(seq, Rooted()); | ~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:468:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf, Tag > > >, void>::Type = void; Fastq = Tag]' 468 | writeWrappedString(target, seq, lineLength); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const Tag&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TagSpec = TagFastq_]' 423 | writeRecord(file.iter, meta, seq, qual, Tag(), context(file).options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const TagSelector&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]' 506 | writeRecord(file, meta, seq, qual, TFormat()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = FormattedFile, Tag >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf >, IsSequence >, void>::Type = void; typename TFile::TStream = VirtualStream, std::char_traits >]' 519 | writeRecord(file, meta, seq, qual, file.format); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:24: required from here 424 | writeRecord(outFile, id, infix(seqCopy, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TSequence = Segment >, InfixSegment>; TSize = int]' 489 | TIter iter = begin(seq, Rooted()); | ~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:475:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf, Tag > > >, void>::Type = void; Fastq = Tag]' 475 | writeWrappedString(target, qual, lineLength); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const Tag&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TagSpec = TagFastq_]' 423 | writeRecord(file.iter, meta, seq, qual, Tag(), context(file).options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const TagSelector&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]' 506 | writeRecord(file, meta, seq, qual, TFormat()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = FormattedFile, Tag >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf >, IsSequence >, void>::Type = void; typename TFile::TStream = VirtualStream, std::char_traits >]' 519 | writeRecord(file, meta, seq, qual, file.format); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:24: required from here 424 | writeRecord(outFile, id, infix(seqCopy, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | : data_container(_toPointer(container_)), | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]' 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TSequence = Segment, Alloc<> >, InfixSegment>; TSize = int]' 489 | TIter iter = begin(seq, Rooted()); | ~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:468:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf, Tag > > >, void>::Type = void; Fastq = Tag]' 468 | writeWrappedString(target, seq, lineLength); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const Tag&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TagSpec = TagFastq_]' 423 | writeRecord(file.iter, meta, seq, qual, Tag(), context(file).options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const TagSelector&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]' 506 | writeRecord(file, meta, seq, qual, TFormat()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = FormattedFile, Tag >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf >, IsSequence >, void>::Type = void; typename TFile::TStream = VirtualStream, std::char_traits >]' 519 | writeRecord(file, meta, seq, qual, file.format); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:24: required from here 424 | writeRecord(outFile, id, infix(seqCopy, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 117 | : data_container(_toPointer(container_)), | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]' 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TSequence = Segment >, InfixSegment>; TSize = int]' 489 | TIter iter = begin(seq, Rooted()); | ~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:475:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf, Tag > > >, void>::Type = void; Fastq = Tag]' 475 | writeWrappedString(target, qual, lineLength); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const Tag&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TagSpec = TagFastq_]' 423 | writeRecord(file.iter, meta, seq, qual, Tag(), context(file).options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const TagSelector&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]' 506 | writeRecord(file, meta, seq, qual, TFormat()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = FormattedFile, Tag >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf >, IsSequence >, void>::Type = void; typename TFile::TStream = VirtualStream, std::char_traits >]' 519 | writeRecord(file, meta, seq, qual, file.format); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:24: required from here 424 | writeRecord(outFile, id, infix(seqCopy, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' 257 | _open(*this, fileName, openMode, True()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' 257 | _open(*this, fileName, openMode, True()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' 257 | _open(*this, fileName, openMode, True()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' 257 | _open(*this, fileName, openMode, True()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' 257 | _open(*this, fileName, openMode, True()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Built target pair_align_global_0000 make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/samcat /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/samcat /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/samcat/CMakeFiles/samcat.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/samcat && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o -MF CMakeFiles/samcat.dir/samcat.cpp.o.d -o CMakeFiles/samcat.dir/samcat.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = Segment >, PrefixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::Segment >, seqan::PrefixSegment>]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = Segment >, SuffixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::Segment >, seqan::SuffixSegment>]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = long int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const long int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = long int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = long int; TSource = Segment >, PrefixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const long int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = long int; TSource = seqan::Segment >, seqan::PrefixSegment>]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = long int; TSource = Segment >, SuffixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const long int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = long int; TSource = seqan::Segment >, seqan::SuffixSegment>]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:35: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 2%] Linking CXX executable ../../bin/rabema_evaluate cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_evaluate.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic -Wl,--dependency-file=CMakeFiles/rabema_evaluate.dir/link.d CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -o ../../bin/rabema_evaluate -lrt -lz -lbz2 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Built target rabema_evaluate make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/searchjoin /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/searchjoin/CMakeFiles/s4_search.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/searchjoin/CMakeFiles/s4_search.dir/search.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/searchjoin && /usr/bin/c++ -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/searchjoin/CMakeFiles/s4_search.dir/search.cpp.o -MF CMakeFiles/s4_search.dir/search.cpp.o.d -o CMakeFiles/s4_search.dir/search.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp [ 2%] Linking CXX executable ../../bin/razers3_simulate_reads cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3_simulate_reads.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic -Wl,--dependency-file=CMakeFiles/razers3_simulate_reads.dir/link.d CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -o ../../bin/razers3_simulate_reads -lrt -lz -lbz2 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Built target razers3_simulate_reads make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/searchjoin /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/searchjoin/CMakeFiles/s4_join.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/searchjoin && /usr/bin/c++ -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o -MF CMakeFiles/s4_join.dir/join.cpp.o.d -o CMakeFiles/s4_join.dir/join.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/parallel/base.h:36, from /usr/include/c++/14/parallel/algobase.h:40, from /usr/include/c++/14/parallel/algorithm:36, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:48: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:36: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/parallel/base.h:36, from /usr/include/c++/14/parallel/algobase.h:40, from /usr/include/c++/14/parallel/algorithm:36, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:48: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ [ 2%] Linking CXX executable ../../bin/razers3_quality2prob cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3_quality2prob.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic -Wl,--dependency-file=CMakeFiles/razers3_quality2prob.dir/link.d CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -o ../../bin/razers3_quality2prob -lrt -lz -lbz2 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Built target razers3_quality2prob make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/seqan_tcoffee /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/seqan_tcoffee /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/seqan_tcoffee && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.13.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -MF CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o.d -o CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:46: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:46: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:22: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ c++: fatal error: Killed signal terminated program cc1plus compilation terminated. make[4]: *** [apps/razers3/CMakeFiles/razers3.dir/build.make:82: apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o] Error 1 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:21268: apps/razers3/CMakeFiles/razers3.dir/all] Error 2 make[3]: *** Waiting for unfinished jobs.... [ 2%] Building CXX object apps/razers/CMakeFiles/razers.dir/param_tabs.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers/CMakeFiles/razers.dir/param_tabs.cpp.o -MF CMakeFiles/razers.dir/param_tabs.cpp.o.d -o CMakeFiles/razers.dir/param_tabs.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/param_tabs.cpp /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:355:10: required from 'void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 355 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 264 | index(joiner); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:319:37: required from here 319 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Exact()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:142: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 264 | index(joiner); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:41: required from here 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:279:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 279 | prepare(joiner, db); | ~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:41: required from here 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:355:10: required from 'void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 355 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 264 | index(joiner); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:332:37: required from here 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Exact()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 264 | index(joiner); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:41: required from here 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:279:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 279 | prepare(joiner, db); | ~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:41: required from here 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:355:10: required from 'void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 355 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 264 | index(joiner); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:357:37: required from here 357 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Exact()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 264 | index(joiner); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:41: required from here 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:279:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 279 | prepare(joiner, db); | ~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:41: required from here 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:355:10: required from 'void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 355 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 264 | index(joiner); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:370:37: required from here 370 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Exact()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 264 | index(joiner); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:41: required from here 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:279:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 279 | prepare(joiner, db); | ~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:41: required from here 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:138: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 311 | _historyClear(it); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:41: required from here 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 311 | _historyClear(it); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:41: required from here 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 311 | _historyClear(it); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:41: required from here 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 311 | _historyClear(it); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:41: required from here 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]' 2236 | _clear(it); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 312 | clear(it); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:41: required from here 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]' 2236 | _clear(it); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 312 | clear(it); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:41: required from here 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]' 2236 | _clear(it); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 312 | clear(it); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:41: required from here 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]' 2236 | _clear(it); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 312 | clear(it); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:41: required from here 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]' 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' 78 | return _verify(*this, dbId, queryId, delegate); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 791 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:29: required from here 311 | return runJoiner(options, TDbDna(), Nothing(), Online()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]' 515 | return begin(cont, Rooted()); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter, StreamIterator > >; TContainer = Segment >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = char]' 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:132:10: required from 'void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]' 132 | write(writer.outputIt, id1); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:197:21: required from 'bool close(Writer >&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>]' 197 | _writeRecord(writer, writer.db.ids[dbId], writer.db.ids[dbId]); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:293:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' 293 | close(writer); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:29: required from here 311 | return runJoiner(options, TDbDna(), Nothing(), Online()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter > >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]' 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' 78 | return _verify(*this, dbId, queryId, delegate); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 791 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:349:29: required from here 349 | return runJoiner(options, TDbGeo(), Nothing(), Online()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]' 377 | _historyPush(it); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]' 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 432 | if (_moveIteratorsDown(finder, TStage())) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]' 1311 | if (_pushState(finder, TStage())) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 611 | _find(finderExt, dbFinder, StageInitial_()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:41: required from here 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]' 377 | _historyPush(it); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Truncated]' 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 432 | if (_moveIteratorsDown(finder, TStage())) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]' 1311 | if (_pushState(finder, TStage())) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 611 | _find(finderExt, dbFinder, StageInitial_()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:41: required from here 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]' 377 | _historyPush(it); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]' 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 432 | if (_moveIteratorsDown(finder, TStage())) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]' 1311 | if (_pushState(finder, TStage())) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 611 | _find(finderExt, dbFinder, StageInitial_()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:41: required from here 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]' 377 | _historyPush(it); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Truncated]' 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 432 | if (_moveIteratorsDown(finder, TStage())) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]' 1311 | if (_pushState(finder, TStage())) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 611 | _find(finderExt, dbFinder, StageInitial_()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:41: required from here 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]' 377 | _historyPush(it); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]' 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 432 | if (_moveIteratorsDown(finder, TStage())) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]' 1311 | if (_pushState(finder, TStage())) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 611 | _find(finderExt, dbFinder, StageInitial_()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:41: required from here 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]' 377 | _historyPush(it); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Truncated]' 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 432 | if (_moveIteratorsDown(finder, TStage())) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]' 1311 | if (_pushState(finder, TStage())) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 611 | _find(finderExt, dbFinder, StageInitial_()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:41: required from here 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]' 377 | _historyPush(it); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]' 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 432 | if (_moveIteratorsDown(finder, TStage())) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]' 1311 | if (_pushState(finder, TStage())) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 611 | _find(finderExt, dbFinder, StageInitial_()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:41: required from here 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]' 377 | _historyPush(it); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Truncated]' 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 432 | if (_moveIteratorsDown(finder, TStage())) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]' 1311 | if (_pushState(finder, TStage())) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 611 | _find(finderExt, dbFinder, StageInitial_()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:41: required from here 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc > >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' 117 | : data_container(_toPointer(container_)), | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]' 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]' 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' 78 | return _verify(*this, dbId, queryId, delegate); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 791 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:29: required from here 311 | return runJoiner(options, TDbDna(), Nothing(), Online()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 117 | : data_container(_toPointer(container_)), | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]' 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]' 515 | return begin(cont, Rooted()); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter, StreamIterator > >; TContainer = Segment >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = char]' 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:132:10: required from 'void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]' 132 | write(writer.outputIt, id1); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:197:21: required from 'bool close(Writer >&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>]' 197 | _writeRecord(writer, writer.db.ids[dbId], writer.db.ids[dbId]); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:293:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' 293 | close(writer); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:29: required from here 311 | return runJoiner(options, TDbDna(), Nothing(), Online()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment > >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]' 117 | : data_container(_toPointer(container_)), | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]' 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter > >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]' 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' 78 | return _verify(*this, dbId, queryId, delegate); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 791 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:349:29: required from here 349 | return runJoiner(options, TDbGeo(), Nothing(), Online()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:282:10: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' 282 | index(searcher); | ~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:39: required from here 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:142: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:323:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' 323 | prepare(searcher, query); | ~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:39: required from here 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:282:10: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' 282 | index(searcher); | ~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:39: required from here 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:323:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' 323 | prepare(searcher, query); | ~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:39: required from here 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:405:10: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' 405 | index(searcher); | ~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:39: required from here 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:449:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' 449 | prepare(searcher, queryLong); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:39: required from here 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:405:10: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' 405 | index(searcher); | ~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:39: required from here 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:449:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' 449 | prepare(searcher, queryLong); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:39: required from here 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:138: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 311 | _historyClear(it); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' 330 | execute(searcher); | ~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:39: required from here 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 311 | _historyClear(it); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' 330 | execute(searcher); | ~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:39: required from here 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 311 | _historyClear(it); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' 456 | execute(searcher); | ~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:39: required from here 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 311 | _historyClear(it); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' 456 | execute(searcher); | ~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:39: required from here 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]' 2236 | _clear(it); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 312 | clear(it); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' 330 | execute(searcher); | ~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:39: required from here 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ make[4]: *** Deleting file 'apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o' make[4]: *** [apps/searchjoin/CMakeFiles/s4_join.dir/build.make:82: apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o] Terminated make[4]: *** wait: No child processes. Stop. make[4]: *** Waiting for unfinished jobs.... make[4]: *** wait: No child processes. Stop. make[4]: *** [apps/samcat/CMakeFiles/samcat.dir/build.make:82: apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o] Terminated make[4]: *** [apps/searchjoin/CMakeFiles/s4_search.dir/build.make:82: apps/searchjoin/CMakeFiles/s4_search.dir/search.cpp.o] Terminated make[4]: *** wait: No child processes. Stop. make[4]: *** Waiting for unfinished jobs.... make[4]: *** wait: No child processes. Stop. make[3]: *** [CMakeFiles/Makefile2:21556: apps/searchjoin/CMakeFiles/s4_join.dir/all] Terminated make[3]: *** [CMakeFiles/Makefile2:21460: apps/sam2matrix/CMakeFiles/sam2matrix.dir/all] Error 2 make[3]: *** [CMakeFiles/Makefile2:21492: apps/samcat/CMakeFiles/samcat.dir/all] Terminated make[3]: *** [CMakeFiles/Makefile2:21524: apps/searchjoin/CMakeFiles/s4_search.dir/all] Terminated make[4]: *** [apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make:82: apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o] Terminated make[3]: *** [CMakeFiles/Makefile2:21588: apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/all] Terminated make[3]: *** [CMakeFiles/Makefile2:21396: apps/sak/CMakeFiles/sak.dir/all] Error 2 make[4]: *** [apps/rep_sep/CMakeFiles/rep_sep.dir/build.make:82: apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o] Terminated make[3]: *** [CMakeFiles/Makefile2:21364: apps/rep_sep/CMakeFiles/rep_sep.dir/all] Terminated make[4]: *** [apps/razers/CMakeFiles/razers.dir/build.make:82: apps/razers/CMakeFiles/razers.dir/razers.cpp.o] Terminated make[4]: *** [apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make:82: apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o] Terminated make[1]: *** [debian/rules:76: override_dh_auto_build-arch] Terminated make[4]: *** [apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make:82: apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o] Terminated make[2]: *** [Makefile:149: all] Terminated Terminated make[4]: *** [apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make:82: apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o] Terminated make: *** [debian/rules:45: binary] Terminated I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem W: Stray processes left from build: * system-pbuilder-build-seqan2_2.4.0\x2bdfsg\x2d16-995300.slice - Slice /system/pbuilder/build/seqan2_2.4.0+dfsg-16/995300 Loaded: loaded Active: active since Thu 2025-06-05 18:42:22 -12; 10min ago Tasks: 3 Memory: 1.6G CPU: 35min 36.774s CGroup: /system.slice/system-pbuilder.slice/system-pbuilder-build.slice/system-pbuilder-build-seqan2_2.4.0\x2bdfsg\x2d16.slice/system-pbuilder-build-seqan2_2.4.0\x2bdfsg\x2d16-995300.slice `-run-r8298d124f8bf42ebab0552b688b85369.scope |-1004463 /usr/libexec/gcc/aarch64-linux-gnu/14/cc1plus -quiet -I /build/reproducible-path/seqan2-2.4.0+dfsg/include -imultiarch aarch64-linux-gnu -MD CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.d -MF CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o.d -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o -D_GNU_SOURCE -D_REENTRANT -D "SEQAN_APP_VERSION=\"1.3.8\"" -D "SEQAN_DATE=\"\"" -D SEQAN_DISABLE_VERSION_CHECK -D SEQAN_HAS_BZIP2=1 -D SEQAN_HAS_EXECINFO=1 -D SEQAN_HAS_OPENMP=1 -D SEQAN_HAS_ZLIB=1 -D "SEQAN_REVISION=\"tarball\"" -D SUFFIX_GAP_BOTTOM=0 -D SUFFIX_GAP_LEFT=1 -D SUFFIX_GAP_RIGHT=1 -D SUFFIX_GAP_TOP=0 -D _FILE_OFFSET_BITS=64 -D _LARGEFILE_SOURCE -D NDEBUG -D _FORTIFY_SOURCE=2 -D SEQAN_GLOBAL_EXCEPTION_HANDLER=1 /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp -quiet -dumpdir CMakeFiles/pair_align_global_0110.dir/ -dumpbase pair_align_global.cpp.cpp -dumpbase-ext .cpp -mbranch-protection=standard -mlittle-endian -mabi=lp64 -g -O2 -O3 -Wformat=1 -Werror=format-security -Wdate-time -Wextra -Wall -Wpedantic -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -fopenmp -fasynchronous-unwind-tables -o /tmp/ccDJyp0C.s |-1017679 /usr/libexec/gcc/aarch64-linux-gnu/14/cc1plus -quiet -I /build/reproducible-path/seqan2-2.4.0+dfsg/include -imultiarch aarch64-linux-gnu -MD CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.d -MF CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o.d -MT apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -D_GNU_SOURCE -D_REENTRANT -D "SEQAN_APP_VERSION=\"1.13.8\"" -D "SEQAN_DATE=\"\"" -D SEQAN_DISABLE_VERSION_CHECK -D SEQAN_HAS_BZIP2=1 -D SEQAN_HAS_EXECINFO=1 -D SEQAN_HAS_OPENMP=1 -D SEQAN_HAS_ZLIB=1 -D "SEQAN_REVISION=\"tarball\"" -D _FILE_OFFSET_BITS=64 -D _LARGEFILE_SOURCE -D NDEBUG -D _FORTIFY_SOURCE=2 -D SEQAN_GLOBAL_EXCEPTION_HANDLER=1 /build/reproducible-path/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp -quiet -dumpdir CMakeFiles/seqan_tcoffee.dir/ -dumpbase seqan_tcoffee.cpp.cpp -dumpbase-ext .cpp -mbranch-protection=standard -mlittle-endian -mabi=lp64 -g -O2 -O3 -Wformat=1 -Werror=format-security -Wdate-time -Wextra -Wall -Wpedantic -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -fopenmp -fasynchronous-unwind-tables -o /tmp/ccCqTD7G.s `-1017771 as -I /build/reproducible-path/seqan2-2.4.0+dfsg/include --gdwarf-5 -EL -mabi=lp64 -o CMakeFiles/rep_sep.dir/rep_sep.cpp.o /tmp/ccwJxAWd.s Jun 05 18:42:22 codethink04-arm64 systemd[1]: Created slice system-pbuilder-build-seqan2_2.4.0\x2bdfsg\x2d16-995300.slice - Slice /system/pbuilder/build/seqan2_2.4.0+dfsg-16/995300. I: cleaning the build env I: removing directory /srv/workspace/pbuilder/995300 and its subdirectories Starting cleanup. All cleanup done. Fri Jun 6 06:53:17 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-jnGaWFDl, removing. /srv/reproducible-results/rbuild-debian/r-b-build.g2xuQ2g3: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Jun 6 06:53 b1 drwxr-xr-x 2 jenkins jenkins 4096 Jun 6 06:42 b2 -rw------- 1 jenkins jenkins 3455 Jun 6 06:42 rbuildlog.UxslTan -rw-r--r-- 1 jenkins jenkins 2321 Jan 15 2024 seqan2_2.4.0+dfsg-16.dsc /srv/reproducible-results/rbuild-debian/r-b-build.g2xuQ2g3/b1: total 5508 -rw-r--r-- 1 jenkins jenkins 5637402 Jun 6 06:53 build.log /srv/reproducible-results/rbuild-debian/r-b-build.g2xuQ2g3/b2: total 0 Fri Jun 6 06:53:19 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jun 5 18:42:15 -12 2025 I: pbuilder-time-stamp: 1749192135 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [seqan2_2.4.0+dfsg-16.dsc] I: copying [./seqan2_2.4.0+dfsg.orig.tar.xz] I: copying [./seqan2_2.4.0+dfsg-16.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./seqan2_2.4.0+dfsg-16.dsc: no acceptable signature found dpkg-source: info: extracting seqan2 in seqan2-2.4.0+dfsg dpkg-source: info: unpacking seqan2_2.4.0+dfsg.orig.tar.xz dpkg-source: info: unpacking seqan2_2.4.0+dfsg-16.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling dpkg-source: info: applying skip-seqan-revision dpkg-source: info: applying fix-version_check-test dpkg-source: info: applying skip-some-apps-on-some-archs dpkg-source: info: applying tweak_readmes dpkg-source: info: applying install_fiona_illumina dpkg-source: info: applying ctdVersion.patch dpkg-source: info: applying fix_manpage_formatting.patch dpkg-source: info: applying no-unaligned-access.patch dpkg-source: info: applying ia64_yield dpkg-source: info: applying python3 dpkg-source: info: applying fix_python3_tests I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/995300/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='fc1dfb2a0a5c4f3380a78027dae3a16a' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='995300' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.g2xuQ2g3/pbuilderrc_CUcN --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.g2xuQ2g3/b1 --logfile b1/build.log seqan2_2.4.0+dfsg-16.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-37-cloud-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 12 19:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/995300/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), python3, cmake, fakeroot, zlib1g-dev, libbz2-dev, libbam-dev, libboost-dev, help2man, ctdconverter dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19964 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on ctdconverter; however: Package ctdconverter is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} ctdconverter{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbam-dev{a} libboost-dev{a} libboost1.83-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgcrypt20{a} libgnutls30t64{a} libgpg-error0{a} libgssapi-krb5-2{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} libxslt1.1{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} procps{a} python3{a} python3-ctdopts{a} python3-lxml{a} python3-minimal{a} python3-ruamel.yaml{a} python3-ruamel.yaml.clib{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpg-error-l10n libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix python3-bs4 python3-cssselect python3-html5lib wget 0 packages upgraded, 86 newly installed, 0 to remove and 0 not upgraded. Need to get 49.3 MB of archives. After unpacking 310 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.4-1 [855 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.1-1 [93.3 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.4-1 [2002 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.4-1 [27.3 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 media-types all 13.0.0 [29.3 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025b-3 [260 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.8-2 [21.3 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.4-1 [1892 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.4-1 [756 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.4-1 [10.2 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.4-1 [28.3 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-8 [63.0 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-8 [873 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2 [241 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-5 [93.8 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.6-2 [2268 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-1 [629 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-3 [323 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1+b1 [24.2 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 41 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-2 [107 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1.1 [71.4 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.14.1-1 [360 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.6-1 [131 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.50.0-2 [148 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.6-2 [9906 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-ctdopts all 1.5-5 [22.5 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libgpg-error0 arm64 1.51-4 [78.5 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libgcrypt20 arm64 1.11.0-7 [742 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libxslt1.1 arm64 1.1.35-1.2 [221 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-lxml arm64 5.4.0-1 [1139 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-ruamel.yaml.clib arm64 0.2.12+ds-1+b1 [117 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 python3-ruamel.yaml all 0.18.10+ds-1 [147 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 ctdconverter all 2.1-8 [27.9 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 75 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2 [1611 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libbam-dev arm64 0.1.19+dfsg-6 [110 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-4.2 [10.6 MB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 86 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Fetched 49.3 MB in 0s (141 MB/s) Preconfiguring packages ... Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19964 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.4-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.4-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.7.1-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.1-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.4-1_arm64.deb ... Unpacking python3.13-minimal (3.13.4-1) ... Setting up libpython3.13-minimal:arm64 (3.13.4-1) ... Setting up libexpat1:arm64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.4-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.4-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.4-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.4-1_arm64.deb ... Unpacking python3.13 (3.13.4-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.13.4-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.13.4-1) ... Setting up python3-minimal (3.13.4-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21328 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.4-1_arm64.deb ... Unpacking python3 (3.13.4-1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-8_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-8) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.4-8_arm64.deb ... Unpacking procps (2:4.0.4-8) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../05-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. 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Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../18-cmake-data_3.31.6-2_all.deb ... Unpacking cmake-data (3.31.6-2) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../19-libxml2_2.12.7+dfsg+really2.9.14-1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-1) ... 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Unpacking libkeyutils1:arm64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../26-libkrb5-3_1.21.3-5_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../27-libgssapi-krb5-2_1.21.3-5_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-5) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../28-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../29-libidn2-0_2.3.8-2_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.8-2) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../30-libsasl2-modules-db_2.1.28+dfsg1-9_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../31-libsasl2-2_2.1.28+dfsg1-9_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:arm64. Preparing to unpack .../32-libldap2_2.6.10+dfsg-1_arm64.deb ... Unpacking libldap2:arm64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../33-libnghttp2-14_1.64.0-1.1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1.1) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../34-libnghttp3-9_1.8.0-1_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.8.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../35-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package libp11-kit0:arm64. Preparing to unpack .../36-libp11-kit0_0.25.5-3_arm64.deb ... Unpacking libp11-kit0:arm64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:arm64. Preparing to unpack .../37-libtasn1-6_4.20.0-2_arm64.deb ... Unpacking libtasn1-6:arm64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:arm64. Preparing to unpack .../38-libgnutls30t64_3.8.9-2_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.9-2) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../39-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../40-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../41-libcurl4t64_8.14.1-1_arm64.deb ... Unpacking libcurl4t64:arm64 (8.14.1-1) ... Selecting previously unselected package libjsoncpp26:arm64. Preparing to unpack .../42-libjsoncpp26_1.9.6-3_arm64.deb ... Unpacking libjsoncpp26:arm64 (1.9.6-3) ... Selecting previously unselected package librhash1:arm64. Preparing to unpack .../43-librhash1_1.4.6-1_arm64.deb ... Unpacking librhash1:arm64 (1.4.6-1) ... Selecting previously unselected package libuv1t64:arm64. Preparing to unpack .../44-libuv1t64_1.50.0-2_arm64.deb ... Unpacking libuv1t64:arm64 (1.50.0-2) ... Selecting previously unselected package cmake. Preparing to unpack .../45-cmake_3.31.6-2_arm64.deb ... Unpacking cmake (3.31.6-2) ... Selecting previously unselected package python3-ctdopts. Preparing to unpack .../46-python3-ctdopts_1.5-5_all.deb ... Unpacking python3-ctdopts (1.5-5) ... Selecting previously unselected package libgpg-error0:arm64. Preparing to unpack .../47-libgpg-error0_1.51-4_arm64.deb ... Unpacking libgpg-error0:arm64 (1.51-4) ... Selecting previously unselected package libgcrypt20:arm64. Preparing to unpack .../48-libgcrypt20_1.11.0-7_arm64.deb ... Unpacking libgcrypt20:arm64 (1.11.0-7) ... Selecting previously unselected package libxslt1.1:arm64. Preparing to unpack .../49-libxslt1.1_1.1.35-1.2_arm64.deb ... Unpacking libxslt1.1:arm64 (1.1.35-1.2) ... Selecting previously unselected package python3-lxml:arm64. Preparing to unpack .../50-python3-lxml_5.4.0-1_arm64.deb ... Unpacking python3-lxml:arm64 (5.4.0-1) ... Selecting previously unselected package python3-ruamel.yaml.clib. Preparing to unpack .../51-python3-ruamel.yaml.clib_0.2.12+ds-1+b1_arm64.deb ... Unpacking python3-ruamel.yaml.clib (0.2.12+ds-1+b1) ... Selecting previously unselected package python3-ruamel.yaml. Preparing to unpack .../52-python3-ruamel.yaml_0.18.10+ds-1_all.deb ... Unpacking python3-ruamel.yaml (0.18.10+ds-1) ... Selecting previously unselected package ctdconverter. Preparing to unpack .../53-ctdconverter_2.1-8_all.deb ... Unpacking ctdconverter (2.1-8) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../54-libdebhelper-perl_13.24.2_all.deb ... 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Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libjsoncpp26:arm64 (1.9.6-3) ... Setting up libproc2-0:arm64 (2:4.0.4-8) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libk5crypto3:arm64 (1.21.3-5) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-9) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:arm64 (1.8.0-1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-8) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... Setting up netbase (6.5) ... Setting up cmake-data (3.31.6-2) ... Setting up librhash1:arm64 (1.4.6-1) ... Setting up libkrb5-3:arm64 (1.21.3-5) ... Setting up libboost-dev:arm64 (1.83.0.2+b2) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... 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Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/seqan2-2.4.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../seqan2_2.4.0+dfsg-16_source.changes dpkg-buildpackage: info: source package seqan2 dpkg-buildpackage: info: source version 2.4.0+dfsg-16 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg' dh_auto_clean find . -type f -name "*.pyc" -delete if [ -d orig ] ; then \ for header in `find orig -name "*generated_forwards.h"` ; do \ mv ${header} `echo $header | sed 's?orig/??'` ; \ done ; \ fi rm -rf orig make[1]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/seqan-apps.substvars debian/libseqan2-dev.substvars debian/files rm -fr -- debian/seqan-apps/ debian/tmp/ debian/libseqan2-dev/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure-arch make[1]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg' # Test seems to fail temporarily (see bug #1058548) find . -name "solution_online_search_finder.cpp*" -delete export DEB_BUILD_ARCH=arm64 ; \ dh_auto_configure --arch -- \ -DSEQAN_STATIC_APPS=False -DSEQAN_NO_DOX=1 \ -DSEQAN_DISABLE_VERSION_CHECK=YES cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DSEQAN_STATIC_APPS=False -DSEQAN_NO_DOX=1 -DSEQAN_DISABLE_VERSION_CHECK=YES .. CMake Warning (dev) at CMakeLists.txt:9 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:16 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Initializing SeqAn Build System... -- Scanning dependencies once in DEVELOP mode... -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Found BZip2: /usr/lib/aarch64-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:359 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:123 (seqan_build_system_init) This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/aarch64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") -- Performing Test CXX14_BUILTIN -- Performing Test CXX14_BUILTIN - Success CMake Warning (dev) at util/cmake/seqan-config.cmake:218 (EXEC_PROGRAM): Policy CMP0153 is not set: The exec_program command should not be called. Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Use execute_process() instead. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:360 (find_package) CMakeLists.txt:123 (seqan_build_system_init) This warning is for project developers. Use -Wno-dev to suppress it. -- Looking for C++ include execinfo.h -- Looking for C++ include execinfo.h - found -- Found Seqan: /build/reproducible-path/seqan2-2.4.0+dfsg/include (found version "2.4.0") -- Selected repository dir: /build/reproducible-path/seqan2-2.4.0+dfsg -- Repository date not determined. -- Repository revision not determined. -- Configuring tests CMake Deprecation Warning at tests/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests CMake Deprecation Warning at tests/align/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/align -- Could NOT find SDE: Intel(R) Software Development Emulator (sde) (missing: SDE_EXECUTABLE SDE_VERSION_STRING) -- Could NOT find Umesimd (missing: UMESIMD_INCLUDE_DIR) -- Performing Test SSE4_SOURCE_RUNS -- Performing Test SSE4_SOURCE_RUNS - Failed -- => Abort simd detection of newer instruction sets -- Performing Test SEQAN_SIMD_SEQANSIMD_SUPPORTED -- Performing Test SEQAN_SIMD_SEQANSIMD_SUPPORTED - Success -- Performing Test SEQANSIMD_AVX512_KNL_SOURCE_RUNS -- Performing Test SEQANSIMD_AVX512_KNL_SOURCE_RUNS - Failed -- Intel Software Development Emulator not found, not building platform emulated tests. -- Intel Software Development Emulator not found, not building platform emulated tests. -- Intel Software Development Emulator not found, not building platform emulated tests. -- Intel Software Development Emulator not found, not building platform emulated tests. CMake Deprecation Warning at tests/align_extend/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/align_extend CMake Deprecation Warning at tests/align_parallel/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/align_parallel -- Could NOT find SDE: Intel(R) Software Development Emulator (sde) (missing: SDE_EXECUTABLE SDE_VERSION_STRING) -- Could NOT find Umesimd (missing: UMESIMD_INCLUDE_DIR) -- Intel Software Development Emulator not found, not building platform emulated tests. -- Intel Software Development Emulator not found, not building platform emulated tests. CMake Deprecation Warning at tests/align_profile/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/align_profile CMake Deprecation Warning at tests/align_split/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/align_split CMake Deprecation Warning at tests/alignment_free/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/alignment_free CMake Deprecation Warning at tests/arg_parse/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/arg_parse CMake Deprecation Warning at tests/bam_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/bam_io CMake Deprecation Warning at tests/basic/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/basic CMake Deprecation Warning at tests/bed_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/bed_io CMake Deprecation Warning at tests/blast/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/blast CMake Deprecation Warning at tests/consensus/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/consensus CMake Deprecation Warning at tests/consensus_v2/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/consensus_v2 CMake Deprecation Warning at tests/find/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/find CMake Deprecation Warning at tests/gff_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/gff_io CMake Deprecation Warning at tests/graph_algorithms/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/graph_algorithms CMake Deprecation Warning at tests/graph_align/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/graph_align CMake Deprecation Warning at tests/graph_msa/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/graph_msa CMake Deprecation Warning at tests/graph_types/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/graph_types CMake Deprecation Warning at tests/index/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/index CMake Deprecation Warning at tests/journaled_set/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/journaled_set CMake Deprecation Warning at tests/journaled_string_tree/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/journaled_string_tree CMake Deprecation Warning at tests/map/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/map CMake Deprecation Warning at tests/misc/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/misc CMake Deprecation Warning at tests/modifier/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/modifier CMake Deprecation Warning at tests/modifier_cyclic_shape/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/modifier_cyclic_shape CMake Deprecation Warning at tests/multiple_translation_units/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/multiple_translation_units CMake Deprecation Warning at tests/parallel/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/parallel CMake Deprecation Warning at tests/parse_lm/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/parse_lm CMake Deprecation Warning at tests/pipe/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/pipe CMake Deprecation Warning at tests/platform/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/platform CMake Deprecation Warning at tests/random/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/random CMake Deprecation Warning at tests/realign/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/realign CMake Deprecation Warning at tests/reduced_aminoacid/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/reduced_aminoacid CMake Deprecation Warning at tests/rna_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/rna_io CMake Deprecation Warning at tests/roi_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/roi_io CMake Deprecation Warning at tests/score/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/score CMake Deprecation Warning at tests/seeds/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/seeds CMake Deprecation Warning at tests/seq_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/seq_io CMake Deprecation Warning at tests/sequence/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/sequence CMake Deprecation Warning at tests/sequence_journaled/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/sequence_journaled CMake Deprecation Warning at tests/simd/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/simd -- Could NOT find SDE: Intel(R) Software Development Emulator (sde) (missing: SDE_EXECUTABLE SDE_VERSION_STRING) -- Could NOT find Umesimd (missing: UMESIMD_INCLUDE_DIR) -- Intel Software Development Emulator not found, not building platform emulated tests. CMake Deprecation Warning at tests/simple_intervals_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/simple_intervals_io CMake Deprecation Warning at tests/statistics/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/statistics CMake Deprecation Warning at tests/store/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/store CMake Deprecation Warning at tests/stream/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/stream CMake Deprecation Warning at tests/swift_local/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/find_swift CMake Deprecation Warning at tests/tabix_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/tabix_io CMake Deprecation Warning at tests/translation/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/translation CMake Deprecation Warning at tests/ucsc_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/test_ucsc_io CMake Deprecation Warning at tests/vcf_io/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring tests/vcf_io -- Configuring demos CMake Deprecation Warning at demos/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.13.4", minimum required is "2.7") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:761 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): util/cmake/SeqAnBuildSystem.cmake:838 (_seqan_setup_demo_test) demos/CMakeLists.txt:15 (seqan_register_demos) This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring apps CMake Deprecation Warning at apps/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at apps/alf/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/alf CMake Deprecation Warning at apps/bs_tools/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/bs_tools CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/bs_tools/CMakeLists.txt:123 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/dfi/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/dfi CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/dfi/CMakeLists.txt:74 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/fiona/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/fiona CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/fiona/CMakeLists.txt:100 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/fx_tools/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/fx_tools CMake Deprecation Warning at apps/gustaf/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/gustaf CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/gustaf/CMakeLists.txt:97 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/insegt/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/insegt CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/insegt/CMakeLists.txt:88 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/mason2/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/mason2 CMake Deprecation Warning at apps/micro_razers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/micro_razers CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/micro_razers/CMakeLists.txt:81 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/ngs_roi/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/ngs_roi CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/ngs_roi/CMakeLists.txt:114 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/pair_align/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/pair_align CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/pair_align/CMakeLists.txt:80 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/param_chooser/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/param_chooser CMake Deprecation Warning at apps/rabema/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/rabema CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/rabema/CMakeLists.txt:110 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/razers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/razers CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/razers/CMakeLists.txt:100 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/razers3/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/razers3 CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/razers3/CMakeLists.txt:127 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/razers3/CMakeLists.txt:128 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/rep_sep/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/rep_sep CMake Deprecation Warning at apps/sak/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/sak CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/sak/CMakeLists.txt:86 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/sam2matrix/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/sam2matrix CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/sam2matrix/CMakeLists.txt:74 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/samcat/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/samcat CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/samcat/CMakeLists.txt:81 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/searchjoin/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/searchjoin CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/searchjoin/CMakeLists.txt:84 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/seqan_tcoffee/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/seqan_tcoffee CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/seqan_tcoffee/CMakeLists.txt:73 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/seqcons2/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/seqcons2 CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/seqcons2/CMakeLists.txt:80 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/sgip/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/sgip CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/sgip/CMakeLists.txt:80 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/snp_store/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/snp_store CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/snp_store/CMakeLists.txt:89 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/splazers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/splazers CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/splazers/CMakeLists.txt:87 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/stellar/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/stellar CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/stellar/CMakeLists.txt:79 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/tree_recon/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/tree_recon CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/tree_recon/CMakeLists.txt:73 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/yara/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring apps/yara CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/yara/CMakeLists.txt:188 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done (9.9s) -- Generating done (0.9s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg' rm -f debian/seqan-apps.debhelper.log debian/rules override_dh_auto_configure-indep make[1]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg' dh_auto_configure --indep -B build -- \ -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY -DSEQAN_NO_DOX=1 cd build && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY -DSEQAN_NO_DOX=1 .. CMake Warning (dev) at CMakeLists.txt:9 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:16 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Initializing SeqAn Build System... -- Selected repository dir: /build/reproducible-path/seqan2-2.4.0+dfsg -- Repository date not determined. -- Repository revision not determined. -- Configuring done (0.6s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/seqan2-2.4.0+dfsg/build make[1]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg' rm -f debian/libseqan2-dev.debhelper.log debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg' dh_auto_build --arch "" cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/seqan2-2.4.0+dfsg -B/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg 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apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/depend make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make[4]: 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'/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/depend make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/depend [ 0%] Built target seqan_library make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_local.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/DependInfo.cmake "--color=" make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/mason_options.cpp.o make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/depend cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/methylation_levels.cpp.o make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/DependInfo.cmake "--color=" [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/genomic_variants.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/genomic_variants.cpp.o -MF CMakeFiles/mason_sim.dir/genomic_variants.cpp.o.d -o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_454.cpp.o make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/mason_options.cpp.o -MF CMakeFiles/mason_sim.dir/mason_options.cpp.o.d -o CMakeFiles/mason_sim.dir/mason_options.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/external_split_merge.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/methylation_levels.cpp.o -MF CMakeFiles/mason_sim.dir/methylation_levels.cpp.o.d -o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o -MF CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o.d -o CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/external_split_merge.cpp.o -MF CMakeFiles/mason_sim.dir/external_split_merge.cpp.o.d -o CMakeFiles/mason_sim.dir/external_split_merge.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.cpp make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_base.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_454.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_454.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_454.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_base.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_base.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_base.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o -MF CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o.d -o CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:55: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.h:49: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:58, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:41: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:46: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:52: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:53: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.h:53: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:53, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:53, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:45: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(String&, const Graph&, const TPropertyMap&, TValue) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TValue = int; TCargo = GenomicInterval]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1502:18: required from 'void seqan::findIntervals(String&, const IntervalTree&, TValue2) [with TValue = int; TCargo = GenomicInterval; TValue2 = int]' 1502 | findIntervals(result, it.g, it.pm, query); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:718:18: required from here 718 | findIntervals(intervals, svIntervalTree, svPos); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] 1441 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] 1453 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] 1475 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = signed char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = signed char]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:620:16, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const signed char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = signed char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short int; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = signed char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = signed char]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:620:16, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const signed char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = signed char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]', inlined from 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_sam.h:320:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_sam.h:363:43: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_genome.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_genome.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_genome.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:42: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ [ 0%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -MF CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o.d -o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:106:14: required from here 106 | if (!open(stream, filename)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:106:14: required from here 106 | if (!open(stream, filename)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:106:14: required from here 106 | if (!open(stream, filename)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:153:56: required from here 153 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:140:13: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:140:13: required from 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:153:56: required from here 153 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:46: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:98:7: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]' 98 | class ModifiedIterator > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:59:25: required from 'void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]' 59 | TFragIter it = begin(frag, seqan::Standard()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:153:26: required from here 153 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:264:56: required from here 264 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:140:13: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 512 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:663:20: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::end(ModifiedString&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]' 663 | TResult tmp(end(host(me), tag_)); | ~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:458:102: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]' 458 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); | ~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:59:25: required from 'void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]' 59 | TFragIter it = begin(frag, seqan::Standard()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:153:26: required from here 153 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:140:13: required from 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:264:56: required from here 264 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:46: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:98:7: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]' 98 | class ModifiedIterator > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:193:25: required from 'void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]' 193 | TFragIter it = begin(frag, seqan::Standard()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:264:26: required from here 264 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 512 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:663:20: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::end(ModifiedString&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]' 663 | TResult tmp(end(host(me), tag_)); | ~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:458:102: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]' 458 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); | ~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:193:25: required from 'void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]' 193 | TFragIter it = begin(frag, seqan::Standard()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:264:26: required from here 264 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:167:18: required from here 167 | if (!open(vcfFileIn, toCString(vcfFileName))) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:40: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:167:18: required from here 167 | if (!open(vcfFileIn, toCString(vcfFileName))) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Built target pair_align_lcs make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/DependInfo.cmake "--color=" /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]', inlined from 'void VcfMaterializer::_appendToVariantsBnd(Variants&, const std::vector&)' at /build/reproducible-path/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:608:69: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In member function 'void VcfMaterializer::_appendToVariantsBnd(Variants&, const std::vector&)': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 0%] Linking CXX static library libmason_sim.a cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/cmake -P CMakeFiles/mason_sim.dir/cmake_clean_target.cmake cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_sim.dir/link.txt --verbose=1 /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /usr/bin/ar qc libmason_sim.a CMakeFiles/mason_sim.dir/external_split_merge.cpp.o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o CMakeFiles/mason_sim.dir/mason_options.cpp.o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o CMakeFiles/mason_sim.dir/simulate_454.cpp.o CMakeFiles/mason_sim.dir/simulate_base.cpp.o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o /usr/bin/ranlib libmason_sim.a make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Built target mason_sim make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Built target pair_align_global_0001 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 0%] Built target pair_align_global_1111 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target pair_align_global_0010 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target pair_align_global_0011 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target pair_align_global_1001 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' 86 | if (!open(inFile, fileName)) | ~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' 289 | _initAlignParams(options, sc, alg, spec); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target pair_align_global_1010 make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/param_chooser /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/param_chooser/CMakeFiles/param_chooser.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/param_chooser/CMakeFiles/param_chooser.dir/param_chooser.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/param_chooser && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/param_chooser/CMakeFiles/param_chooser.dir/param_chooser.cpp.o -MF CMakeFiles/param_chooser.dir/param_chooser.cpp.o.d -o CMakeFiles/param_chooser.dir/param_chooser.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::read(Score >&, TSourceIter&, const ScoreMatrixFile&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:140:79, inlined from 'void seqan::read(Score >&, TSourceIter&) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag; TSourceIter = Iter >, StreamIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:9, inlined from 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:9: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::loadScoreMatrix(Score >&, const char*) [with TValue = int; TSequenceValue = SimpleType; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:32: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:33, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:39: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:30, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:34: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:676:44: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 676 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:704:47: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 704 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:730:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 730 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:748:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 748 | struct LessSplicedScore : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:770:45: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 770 | struct LessSplicedScoreGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:32: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:36: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h: In instantiation of 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1658:15: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2250:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1430:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 1430 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:222: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1653:13: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1653 | while (find(swiftFinder, swiftPattern, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2242:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2242 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:87: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1653:13: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1653 | while (find(swiftFinder, swiftPattern, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2245:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2245 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1430:19: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]' 1430 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1658:15: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2250:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1431:13: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]' 1431 | TReadRev readRev(readSet[rseqNo]); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1658:15: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2250:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1653:13: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1653 | while (find(swiftFinder, swiftPattern, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2253:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2253 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1653:13: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1653 | while (find(swiftFinder, swiftPattern, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2256:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2256 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 385 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]' 301 | : data_iterator(begin(haystack, Rooted())) | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1399:15: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]' 1399 | TMyersFinder myersFinder(inf); | ^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1658:15: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2250:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:72:7: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]' 72 | class ModifiedIterator | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]' 301 | : data_iterator(begin(haystack, Rooted())) | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1432:19: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]' 1432 | TMyersFinderRev myersFinderRev(infRev); | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1658:15: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2250:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1625:31: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1625 | TReadSet &readSet = host(host(swiftPattern)); | ~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2239:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2239 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]' 278 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1625:31: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1625 | TReadSet &readSet = host(host(swiftPattern)); | ~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2242:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2242 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]' 278 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1625:31: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1625 | TReadSet &readSet = host(host(swiftPattern)); | ~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2245:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2245 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]' 278 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:55, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:28: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1603:45: required from 'bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]' 1603 | TSize haystack_length = length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1636:16: required from 'bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]' 1636 | return find(finder, pattern, state); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1654:16: required from 'bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFindBeginPatternSpec = void]' 1654 | return find(finder, pattern, pattern, minScore); //static cast | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1414:13: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]' 1414 | while (find(myersFinder, myersPattern, minScore)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1658:15: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2250:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 512 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:469:24: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]' 469 | TIterator temp_(end(host(me), Rooted())); | ~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]' 301 | : data_iterator(begin(haystack, Rooted())) | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1432:19: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]' 1432 | TMyersFinderRev myersFinderRev(infRev); | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1658:15: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]' 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2250:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:61: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:21: required from 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]' 599 | return container(hostIterator(me)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1603:45: required from 'bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]' 1603 | TSize haystack_length = length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1636:16: required from 'bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]' 1636 | return find(finder, pattern, state); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1654:16: required from 'bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]' 1654 | return find(finder, pattern, pattern, minScore); //static cast | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:1437:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2076:18: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2250:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>; typename Reference > >::Type = Segment, Alloc<> >, InfixSegment>&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:840:14: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2047:11: required from 'int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2047 | setHost(forwardPatterns[i], indexText(swiftIndex)[i]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2150:24: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:2239:19: required from 'int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]' 2239 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:712:13: required from 'void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]' 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' 1079 | makeSelectedStatsFile(errorDistribution,pm_options); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: required from here 339 | chooseParams(r_options, pm_options); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target pair_align_global_1000 make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/param_chooser /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/param_chooser && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -MF CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o.d -o CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp:45: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp:42: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:33, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:30, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:34: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:676:44: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 676 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:704:47: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 704 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:730:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 730 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:748:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 748 | struct LessSplicedScore : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:770:45: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 770 | struct LessSplicedScoreGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:32: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target pair_align_global_1011 make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/rabema/CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o [ 1%] Built target pair_align_global_0111 cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -MF CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o.d -o CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 1%] Building CXX object apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -MF CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o.d -o CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:11: required from here 604 | if (!open(seqFile, fname) || atEnd(seqFile)) | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:31: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:27: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:36: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:39: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target pair_align_global_1100 make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema/CMakeFiles/rabema_evaluate.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -MF CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o.d -o CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:42: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:105:10: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 105 | std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:254:100: required from here 254 | TModifiedString rRightInterval(infix(errorCurve, rightmostPos, offset + intervalLength)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:72:7: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]' 72 | class ModifiedIterator | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:257:52: required from here 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]' 512 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:469:24: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]' 469 | TIterator temp_(end(host(me), Rooted())); | ~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:257:52: required from here 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]' 385 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:513:97: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]' 513 | typename Iterator, Tag const >::Type temp_(begin(host(me), Rooted())); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:257:91: required from here 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]', inlined from 'bool seqan::parseGappedParams(RazerSOptions&, TFile&, ParamChooserOptions&) [with TFile = std::__cxx11::basic_stringstream; TSpec = RazerSSpec<>]' at /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:829:51: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'bool seqan::parseGappedParams(RazerSOptions&, TFile&, ParamChooserOptions&) [with TFile = std::__cxx11::basic_stringstream; TSpec = RazerSSpec<>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h: In instantiation of 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); | ~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]' 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 558 | _findBeginInit(pattern, needle); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(Pattern >&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers]' 660 | _patternFirstInit(pattern, needle(pattern)); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 255 | _reinitPattern(me); | ~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from 'void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = long unsigned int]' 403 | Pattern pattern(read, -(int)length(read) * 40); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from 'int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 899 | buildErrorCurvePoints(errorCurves[readId], maxError, contig, record.rID, !hasFlagRC(record), | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 900 | readSeq, readId, endPos, readNameStore, options.matchN, TPatternSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:1203:37: required from here 1203 | res = matchesToErrorFunction(errorCurves, readAlignmentDistances, inBam, readNameStore, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1204 | contigNames(context(inBam)), faiIndex, options, MyersUkkonenReads()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 254 | setValue(_dataHost(me), std::forward(ndl)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from 'void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = long unsigned int]' 403 | Pattern pattern(read, -(int)length(read) * 40); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from 'int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 899 | buildErrorCurvePoints(errorCurves[readId], maxError, contig, record.rID, !hasFlagRC(record), | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 900 | readSeq, readId, endPos, readNameStore, options.matchN, TPatternSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:1203:37: required from here 1203 | res = matchesToErrorFunction(errorCurves, readAlignmentDistances, inBam, readNameStore, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1204 | contigNames(context(inBam)), faiIndex, options, MyersUkkonenReads()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: required from 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]' 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); | ~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]' 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 255 | _reinitPattern(me); | ~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from 'void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = long unsigned int]' 403 | Pattern pattern(read, -(int)length(read) * 40); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from 'int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 899 | buildErrorCurvePoints(errorCurves[readId], maxError, contig, record.rID, !hasFlagRC(record), | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 900 | readSeq, readId, endPos, readNameStore, options.matchN, TPatternSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:1203:37: required from here 1203 | res = matchesToErrorFunction(errorCurves, readAlignmentDistances, inBam, readNameStore, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1204 | contigNames(context(inBam)), faiIndex, options, MyersUkkonenReads()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:29: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:33: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]', inlined from 'bool seqan::parseGappedParams(RazerSOptions&, TFile&, ParamChooserOptions&) [with TFile = std::basic_fstream; TSpec = RazerSSpec<>]' at /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:829:51, inlined from 'bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]' at /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:1107:20, inlined from 'int main(int, const char**)' at /build/reproducible-path/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:339:21: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'int main(int, const char**)': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target pair_align_global_1101 make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema/CMakeFiles/rabema_do_search.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/rabema/CMakeFiles/rabema_do_search.dir/do_search.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_do_search.dir/do_search.cpp.o -MF CMakeFiles/rabema_do_search.dir/do_search.cpp.o.d -o CMakeFiles/rabema_do_search.dir/do_search.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(String&, const Graph&, const TPropertyMap&, TValue) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TValue = unsigned int; TCargo = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1502:18: required from 'void seqan::findIntervals(String&, const IntervalTree&, TValue2) [with TValue = unsigned int; TCargo = unsigned int; TValue2 = unsigned int]' 1502 | findIntervals(result, it.g, it.pm, query); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:644:22: required from 'int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 644 | findIntervals(queryResult, intervalTrees[seqId], lastPos); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1003:42: required from 'int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 1003 | int res = benchmarkReadResult(result, currentSamRecords, bamFileIn, currentGsiRecords, | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1004 | faiIndex, refSeqs, refIdMapping, options, tagPattern, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1005 | /*pairedEnd=*/ false); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1401:45: required from here 1401 | res = compareAlignedReadsToReference(result, bamFileIn, faiIndex, refSeqs, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1402 | inGsiIter, options, MyersUkkonenReads()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] 1441 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] 1453 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] 1475 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:44, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:3: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:45: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ [ 1%] Linking CXX executable ../../bin/param_chooser cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/param_chooser && /usr/bin/cmake -E cmake_link_script CMakeFiles/param_chooser.dir/link.txt --verbose=1 In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:11: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic -Wl,--dependency-file=CMakeFiles/param_chooser.dir/link.d CMakeFiles/param_chooser.dir/param_chooser.cpp.o -o ../../bin/param_chooser -lrt -lz -lbz2 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h: In instantiation of 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); | ~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]' 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 558 | _findBeginInit(pattern, needle); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(Pattern >&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers]' 660 | _patternFirstInit(pattern, needle(pattern)); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 255 | _reinitPattern(me); | ~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:623:51: required from 'int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 623 | Pattern pattern(readSeq, -static_cast(length(readSeq)) * 1000); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1003:42: required from 'int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 1003 | int res = benchmarkReadResult(result, currentSamRecords, bamFileIn, currentGsiRecords, | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1004 | faiIndex, refSeqs, refIdMapping, options, tagPattern, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1005 | /*pairedEnd=*/ false); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1401:45: required from here 1401 | res = compareAlignedReadsToReference(result, bamFileIn, faiIndex, refSeqs, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1402 | inGsiIter, options, MyersUkkonenReads()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 1%] Built target param_chooser make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers/CMakeFiles/razers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object apps/razers/CMakeFiles/razers.dir/razers.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers/CMakeFiles/razers.dir/razers.cpp.o -MF CMakeFiles/razers.dir/razers.cpp.o.d -o CMakeFiles/razers.dir/razers.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 254 | setValue(_dataHost(me), std::forward(ndl)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:623:51: required from 'int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 623 | Pattern pattern(readSeq, -static_cast(length(readSeq)) * 1000); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1003:42: required from 'int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 1003 | int res = benchmarkReadResult(result, currentSamRecords, bamFileIn, currentGsiRecords, | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1004 | faiIndex, refSeqs, refIdMapping, options, tagPattern, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1005 | /*pairedEnd=*/ false); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1401:45: required from here 1401 | res = compareAlignedReadsToReference(result, bamFileIn, faiIndex, refSeqs, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1402 | inGsiIter, options, MyersUkkonenReads()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: required from 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]' 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); | ~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]' 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 255 | _reinitPattern(me); | ~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:623:51: required from 'int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 623 | Pattern pattern(readSeq, -static_cast(length(readSeq)) * 1000); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1003:42: required from 'int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' 1003 | int res = benchmarkReadResult(result, currentSamRecords, bamFileIn, currentGsiRecords, | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1004 | faiIndex, refSeqs, refIdMapping, options, tagPattern, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1005 | /*pairedEnd=*/ false); | ~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1401:45: required from here 1401 | res = compareAlignedReadsToReference(result, bamFileIn, faiIndex, refSeqs, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1402 | inGsiIter, options, MyersUkkonenReads()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:41: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ [ 1%] Linking CXX executable ../../bin/test_funcs_param_chooser cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/param_chooser && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_funcs_param_chooser.dir/link.txt --verbose=1 In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic -Wl,--dependency-file=CMakeFiles/test_funcs_param_chooser.dir/link.d CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -o ../../bin/test_funcs_param_chooser -lrt -lz -lbz2 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 1%] Built target test_funcs_param_chooser make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/depend In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3 /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3 /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3/CMakeFiles/razers3.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o -MF CMakeFiles/razers3.dir/razers.cpp.o.d -o CMakeFiles/razers3.dir/razers.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:13: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:105:10: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 105 | std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:43: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:254:100: required from here 254 | TModifiedString rRightInterval(infix(errorCurve, rightmostPos, offset + intervalLength)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:7: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:72:7: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]' 72 | class ModifiedIterator | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:257:52: required from here 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]' 512 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:469:24: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]' 469 | TIterator temp_(end(host(me), Rooted())); | ~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:257:52: required from here 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]' 385 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:513:97: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]' 513 | typename Iterator, Tag const >::Type temp_(begin(host(me), Rooted())); | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:257:91: required from here 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h: In instantiation of 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); | ~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]' 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 558 | _findBeginInit(pattern, needle); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(Pattern >&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers]' 660 | _patternFirstInit(pattern, needle(pattern)); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 255 | _reinitPattern(me); | ~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:27:89: required from here 27 | Pattern pattern(read, -static_cast(length(read))); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Built target pair_align_global_1110 make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3 /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3 /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>; typename Reference > >::Type = Segment, Alloc<> >, InfixSegment>&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:840:14: required from 'void seqan::setValue(Holder >&, const TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]' 840 | set(value(me), value_); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 254 | setValue(_dataHost(me), std::forward(ndl)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:27:89: required from here 27 | Pattern pattern(read, -static_cast(length(read))); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: required from 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]' 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); | ~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]' 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 558 | _findBeginInit(pattern, needle); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(Pattern >&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers]' 660 | _patternFirstInit(pattern, needle(pattern)); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 255 | _reinitPattern(me); | ~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' 452 | setHost(*this, std::forward(ndl)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:27:89: required from here 27 | Pattern pattern(read, -static_cast(length(read))); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/razers3/CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers3/CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -MF CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o.d -o CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:57: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:41: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:1: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:28, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:29: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:7: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ [ 2%] Linking CXX executable ../../bin/rabema_do_search cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_do_search.dir/link.txt --verbose=1 In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic -Wl,--dependency-file=CMakeFiles/rabema_do_search.dir/link.d CMakeFiles/rabema_do_search.dir/do_search.cpp.o -o ../../bin/rabema_do_search -lrt -lz -lbz2 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Built target rabema_do_search make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3 /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3 /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3/CMakeFiles/razers3_quality2prob.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/razers3/CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers3/CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -MF CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o.d -o CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:41: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:696:44: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 696 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:728:47: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 728 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:760:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 760 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:51: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/outputFormat.h:126:44: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 126 | struct LessGPosRNo : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:1: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]' 996 | if (!open(seqFile, toCString(fileNameList[f]))) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]' 1035 | return loadContigs(store, fileNames, loadSeqs); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]' 1043 | return loadContigs(store, fileNames, true); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:21: required from here 120 | if (!loadContigs(store, toCString(referenceFile))) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]' 996 | if (!open(seqFile, toCString(fileNameList[f]))) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]' 1035 | return loadContigs(store, fileNames, loadSeqs); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]' 1043 | return loadContigs(store, fileNames, true); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:21: required from here 120 | if (!loadContigs(store, toCString(referenceFile))) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]' 996 | if (!open(seqFile, toCString(fileNameList[f]))) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]' 1035 | return loadContigs(store, fileNames, loadSeqs); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]' 1043 | return loadContigs(store, fileNames, true); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:21: required from here 120 | if (!loadContigs(store, toCString(referenceFile))) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]' 996 | if (!open(seqFile, toCString(fileNameList[f]))) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]' 1035 | return loadContigs(store, fileNames, loadSeqs); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]' 1043 | return loadContigs(store, fileNames, true); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:21: required from here 120 | if (!loadContigs(store, toCString(referenceFile))) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:845:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 845 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:862:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 862 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:896:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 896 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:934:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 934 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:968:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 968 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1009:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1009 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1046:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1046 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1087:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1087 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1130:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1130 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1174:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1174 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1218:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1218 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]' 996 | if (!open(seqFile, toCString(fileNameList[f]))) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]' 1035 | return loadContigs(store, fileNames, loadSeqs); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]' 1043 | return loadContigs(store, fileNames, true); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:21: required from here 120 | if (!loadContigs(store, toCString(referenceFile))) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = signed char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = signed char]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:620:16, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const signed char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = signed char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short int; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = signed char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = signed char]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:620:16, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const signed char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = signed char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:127:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]', inlined from 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_sam.h:320:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_sam.h:363:43: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:55: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:221:47: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 221 | struct LessPairErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:6: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:83: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:265:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 265 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:321:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 321 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:366:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 366 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:41: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:622:23: required from here 622 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:622:23: required from here 622 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:7: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:23: required from here 785 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:48: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:97: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1348:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1348 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1348:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1348 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1348:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1348 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1351:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1351 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:622:23: required from here 622 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1351:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1351 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1351:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1351 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1356:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1356 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1356:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1356 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1356:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1356 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1359:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1359 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1359:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1359 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1359:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1359 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1362:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1362 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h: In instantiation of 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:492:40: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 492 | if (matchVerify( | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) | ~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1471:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 1471 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1362:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1362 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h: In instantiation of 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1717:15: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]' 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2043:19: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1471:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 1471 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1362:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1362 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro 'SEQAN_DO_PRAGMA' 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:13: note: in expansion of macro 'SEQAN_OMP_PRAGMA' 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:23: required from here 785 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:622:23: required from here 622 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:23: required from here 785 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment, Alloc<> >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 515 | return begin(cont, Rooted()); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter >, StreamIterator > >; TContainer = Segment, Alloc<> >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = SimpleType]' 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const Segment&) [with TStream = VirtualStream >; THost = const String, Alloc<> >; TSpec = InfixSegment]' 789 | write(it, source); | ~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/outputFormat.h:722:12: required from 'void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 722 | file << reads[(*it).rseqNo]; | ~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:232:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 232 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, stats, readNames, readFileNames[0], errorPrbFileName, options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:23: required from here 785 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:622:23: required from here 622 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 385 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:395:32: required from 'seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]' 395 | data_iterator(begin(haystack, Rooted())), haystackEnd(), _needReinit(true), curHit(), endHit(), | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:394:16: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 394 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); | ^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1928:77: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]' 1928 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:222: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2268:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:87: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1699:13: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]' 1699 | while (find(swiftFinder, swiftPattern, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2043:19: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2268:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2271:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1699:13: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]' 1699 | while (find(swiftFinder, swiftPattern, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2043:19: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2271:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1928:77: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]' 1928 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1471:19: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]' 1471 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:492:40: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 492 | if (matchVerify( | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) | ~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 118 | _host(_toPointer(host)), | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1472:13: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]' 1472 | TReadRev readRev(readSet[rseqNo]); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:492:40: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 492 | if (matchVerify( | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) | ~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2279:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2279 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1699:13: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]' 1699 | while (find(swiftFinder, swiftPattern, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2043:19: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2279:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2279 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2282:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2282 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]' 1929 | _patternInit(pattern, errorRate, minLength); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1699:13: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]' 1699 | while (find(swiftFinder, swiftPattern, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2043:19: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2282:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2282 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::QualityExtractor >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:745:69: required from 'void seqan::write(TTarget&, FragmentStore&, Amos) [with TTarget = VirtualStream >; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; Amos = const Tag]' 745 | ModifiedString > quals(fragStore.readSeqStore[idCount]); | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1222:14: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1222 | write(file, store, Amos()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1866:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 1866 | finder.endPos = length(host(finder)); | ~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1934:34: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]' 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1876:41: required from 'bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 1876 | finder.haystackEnd = begin(tmpHost) + (finder.endPos - length(pattern.shape) + 1); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1934:34: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]' 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1845:48: required from 'bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 1845 | hostIterator(finder) = begin(host(finder)) + finder.startPos; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1965:37: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]' 1965 | if (!_nextNonRepeatRange(finder, pattern)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:23: required from here 785 | success = open(options.readFile, toCString(readFileNames[0])); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1866:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 1866 | finder.endPos = length(host(finder)); | ~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1934:34: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]' 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:72:7: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]' 72 | class ModifiedIterator | ^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]' 301 | : data_iterator(begin(haystack, Rooted())) | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1473:19: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]' 1473 | TMyersFinderRev myersFinderRev(infRev); | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:492:40: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 492 | if (matchVerify( | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) | ~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | : data_container(_toPointer(container_)), | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]' 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment, Alloc<> >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 515 | return begin(cont, Rooted()); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter >, StreamIterator > >; TContainer = Segment, Alloc<> >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = SimpleType]' 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const Segment&) [with TStream = VirtualStream >; THost = const String, Alloc<> >; TSpec = InfixSegment]' 789 | write(it, source); | ~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/outputFormat.h:722:12: required from 'void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 722 | file << reads[(*it).rseqNo]; | ~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:232:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 232 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, stats, readNames, readFileNames[0], errorPrbFileName, options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1662:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:87: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:375:32: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 375 | TReadSet &readSetL = host(host(swiftPatternL)); | ~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]' 278 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1666:31: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]' 1666 | TReadSet &readSet = host(host(swiftPattern)); | ~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2043:19: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' 143 | Index(Index const &other): | ^~~~~ [ 2%] Linking CXX executable ../../bin/rabema_prepare_sam cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_prepare_sam.dir/link.txt --verbose=1 /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:375:32: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 375 | TReadSet &readSetL = host(host(swiftPatternL)); | ~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2268:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]' 278 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1666:31: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]' 1666 | TReadSet &readSet = host(host(swiftPattern)); | ~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2043:19: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2268:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:375:32: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 375 | TReadSet &readSetL = host(host(swiftPatternL)); | ~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2271:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]' 278 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1666:31: required from 'void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]' 1666 | TReadSet &readSet = host(host(swiftPattern)); | ~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2043:19: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2271:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1603:45: required from 'bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]' 1603 | TSize haystack_length = length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1636:16: required from 'bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]' 1636 | return find(finder, pattern, state); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1654:16: required from 'bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; TFindBeginPatternSpec = void]' 1654 | return find(finder, pattern, pattern, minScore); //static cast | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1455:13: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]' 1455 | while (find(myersFinder, myersPattern, minScore)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:492:40: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 492 | if (matchVerify( | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) | ~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 512 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:469:24: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]' 469 | TIterator temp_(end(host(me), Rooted())); | ~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]' 301 | : data_iterator(begin(haystack, Rooted())) | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1473:19: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]' 1473 | TMyersFinderRev myersFinderRev(infRev); | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:492:40: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 492 | if (matchVerify( | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) | ~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1662:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:845:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 845 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:862:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 862 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:896:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 896 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:934:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 934 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:968:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 968 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1009:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1009 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1046:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1046 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1087:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1087 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1130:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1130 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1174:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1174 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1218:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1218 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic -Wl,--dependency-file=CMakeFiles/rabema_prepare_sam.dir/link.d CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -o ../../bin/rabema_prepare_sam -lrt -lz -lbz2 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1662:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ [ 2%] Built target rabema_prepare_sam make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/depend /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rep_sep /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rep_sep/CMakeFiles/rep_sep.dir/DependInfo.cmake "--color=" /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/build /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rep_sep && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.1.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o -MF CMakeFiles/rep_sep.dir/rep_sep.cpp.o.d -o CMakeFiles/rep_sep.dir/rep_sep.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1662:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:369:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]' 369 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1845:33: required from 'bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 1845 | hostIterator(finder) = begin(host(finder)) + finder.startPos; | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1965:37: required from 'bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]' 1965 | if (!_nextNonRepeatRange(finder, pattern)) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]' 1913 | return find(finder, pattern, errorRate, 0); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:428:13: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:61: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:21: required from 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]' 599 | return container(hostIterator(me)); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1603:45: required from 'bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]' 1603 | TSize haystack_length = length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1636:16: required from 'bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]' 1636 | return find(finder, pattern, state); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1654:16: required from 'bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]' 1654 | return find(finder, pattern, pattern, minScore); //static cast | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1478:13: required from 'bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]' 1478 | while (find(myersFinderRev, myersPatternRev, maxScore)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:492:40: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 492 | if (matchVerify( | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) | ~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2276:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_shortcuts.h:340:12: required from 'typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = Segment, Alloc<> >, InfixSegment>; typename ReverseComplementString::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]' 340 | return TRevComp(host); | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:936:80: required from 'void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]' 936 | _fillBamSeqAndQual(record.seq, record.qual, reverseComplementString(store.readSeqStore[alignedRead.readId])); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:140:13: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter >, StreamIterator > >; TSequence = Segment, Alloc<> >, InfixSegment>; TSize = int]' 489 | TIter iter = begin(seq, Rooted()); | ~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:740:27: required from 'void seqan::write(TTarget&, FragmentStore&, Amos) [with TTarget = VirtualStream >; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; Amos = const Tag]' 740 | writeWrappedString(iter, fragStore.readSeqStore[idCount], 60); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1222:14: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1222 | write(file, store, Amos()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:98:7: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::begin(const ModifiedString&, Tag) [with THost = const Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]' 98 | class ModifiedIterator > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter >, StreamIterator > >; TSequence = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TSize = int]' 489 | TIter iter = begin(seq, Rooted()); | ~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:746:27: required from 'void seqan::write(TTarget&, FragmentStore&, Amos) [with TTarget = VirtualStream >; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; Amos = const Tag]' 746 | writeWrappedString(iter, quals, 60); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1222:14: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1222 | write(file, store, Amos()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]' 254 | setValue(_dataHost(me), std::forward(ndl)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:1971:11: required from 'int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 1971 | setHost(forwardPatterns[i], indexText(swiftIndex)[i]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2206:24: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]' 887 | create(me, value_); | ~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 135 | assignValue(*this, value_); | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_wotd.h:259:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:394:16: required from 'void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]' 394 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); | ^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:777:21: required from 'int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2203:26: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]' 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.h:2265:19: required from 'int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]' 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:209:25: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:697:26: required from here 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:14: required from here 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3247:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:223: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2785:21: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]' 2785 | _patternInit(filterPattern, options.errorRate); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1088:24: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1088 | _applyFilterOptions(filterPatternL, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:14: required from here 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:222: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2896:17: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]' 2896 | _patternInit(filterPattern, options.errorRate, 0); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1088:24: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1088 | _applyFilterOptions(filterPatternL, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3247:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3247:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = Hamming_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2785:21: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = Hamming_; TOptions = RazerSCoreOptions >]' 2785 | _patternInit(filterPattern, options.errorRate); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1088:24: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1088 | _applyFilterOptions(filterPatternL, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:14: required from here 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2896:17: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]' 2896 | _patternInit(filterPattern, options.errorRate, 0); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1088:24: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1088 | _applyFilterOptions(filterPatternL, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3247:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = signed char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = signed char]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:620:16, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const signed char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = signed char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short int; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = signed char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = signed char]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:620:16, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const signed char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = signed char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:14: required from here 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3247:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3247:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:14: required from here 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]', inlined from 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_sam.h:320:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_sam.h:363:43: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:55, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:32: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:969:48: required from 'bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]' 969 | pattern.finderLength = length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2979:24: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3216:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2785:21: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]' 2785 | _patternInit(filterPattern, options.errorRate); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3026:24: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 3026 | _applyFilterOptions(filterPattern, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3221:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2979:24: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3221:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:2081:73: required from 'bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 2081 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1200:29: required from 'void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1489:38: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:296:20: required from 'void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >; TShape = Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]' 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:751:33: required from 'void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 751 | workVerification(tls, job, splitters); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1033:44: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2785:21: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]' 2785 | _patternInit(filterPattern, options.errorRate); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:872:28: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]' 872 | _applyFilterOptions(filterPattern, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:296:20: required from 'void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]' 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:751:33: required from 'void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 751 | workVerification(tls, job, splitters); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1033:44: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2896:17: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]' 2896 | _patternInit(filterPattern, options.errorRate, 0); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3026:24: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 3026 | _applyFilterOptions(filterPattern, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3216:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2979:24: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3216:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2896:17: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]' 2896 | _patternInit(filterPattern, options.errorRate, 0); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:872:28: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]' 872 | _applyFilterOptions(filterPattern, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:296:20: required from 'void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]' 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:751:33: required from 'void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 751 | workVerification(tls, job, splitters); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1033:44: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:969:48: required from 'bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]' 969 | pattern.finderLength = length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = Hamming_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2785:21: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = Hamming_; TOptions = RazerSCoreOptions >]' 2785 | _patternInit(filterPattern, options.errorRate); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3026:24: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 3026 | _applyFilterOptions(filterPattern, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3221:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:2081:73: required from 'bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 2081 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1200:29: required from 'void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1489:38: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = Hamming_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2785:21: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = Hamming_; TOptions = RazerSCoreOptions >]' 2785 | _patternInit(filterPattern, options.errorRate); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:872:28: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]' 872 | _applyFilterOptions(filterPattern, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2896:17: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]' 2896 | _patternInit(filterPattern, options.errorRate, 0); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3026:24: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 3026 | _applyFilterOptions(filterPattern, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3216:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2896:17: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]' 2896 | _patternInit(filterPattern, options.errorRate, 0); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:872:28: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]' 872 | _applyFilterOptions(filterPattern, options); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2979:24: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3216:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2979:24: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3221:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:296:20: required from 'void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >; TShape = Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]' 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:751:33: required from 'void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 751 | workVerification(tls, job, splitters); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1033:44: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:296:20: required from 'void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]' 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:751:33: required from 'void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 751 | workVerification(tls, job, splitters); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1033:44: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]' 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2979:24: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3146:27: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3216:31: required from 'int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:296:20: required from 'void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]' 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:751:33: required from 'void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 751 | workVerification(tls, job, splitters); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1033:44: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]' 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]' 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2155:18: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2238:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2239:41: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2341:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2342:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:22: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:90: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]' 679 | return begin(me, Tag()) + pos; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]' 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = String, Alloc<> >; TGapAnchors = String, Alloc<> >; TPosition = long int; TCount = unsigned int]' 466 | TIter it = iter(gaps, clippedViewPos); | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_base.h:513:15: required from 'void seqan::insertGap(Gaps&, TPosition) [with TSequence = String, Alloc<> >; TSpec = AnchorGaps, Alloc<> > >; TPosition = long int]' 513 | insertGaps(gaps, clippedViewPos, 1u); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2067:42: required from 'void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TScore = Score >; TShrinkMatches = True]' 2067 | insertGap(gaps, insPos - rBegin); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1221:40: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1221 | convertMatchesToGlobalAlignment(store, scoreType, True()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)' is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)' is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 385 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:395:32: required from 'seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]' 395 | data_iterator(begin(haystack, Rooted())), haystackEnd(), _needReinit(true), curHit(), endHit(), | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:680:20: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 680 | TFilterFinderR filterFinderR(genomeInf, options.repeatLength, 1); | ^~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3247:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:932:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]' 932 | finder.endPos = length(host(finder)); | ~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:975:34: required from 'bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]' 975 | if (!_firstNonRepeatRange(finder, pattern)) return false; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:941:46: required from 'bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]' 941 | finder.haystackEnd = begin(host(finder)) + (finder.endPos - length(pattern.shape) + 1); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:975:34: required from 'bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]' 975 | if (!_firstNonRepeatRange(finder, pattern)) return false; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1866:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 1866 | finder.endPos = length(host(finder)); | ~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:2088:30: required from 'bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 2088 | if (!_firstNonRepeatRange(finder, pattern)) return false; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1200:29: required from 'void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1489:38: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:932:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]' 932 | finder.endPos = length(host(finder)); | ~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:975:34: required from 'bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]' 975 | if (!_firstNonRepeatRange(finder, pattern)) return false; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]' 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1866:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 1866 | finder.endPos = length(host(finder)); | ~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:2088:30: required from 'bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]' 2088 | if (!_firstNonRepeatRange(finder, pattern)) return false; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1200:29: required from 'void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1489:38: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]' 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]' 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]' 250 | return value(me); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:24: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >]' 209 | if ((TVal1)*it1 == (TVal2)*it2) | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement, Alloc<> >, GapAnchor, void>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 529 | _alignAndGetCigarString(cigar, md, contigInfix, readSeq, alignedRead, errors, functor); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]' 905 | alignAndGetCigarString(record.cigar, record.qual, store.contigStore[alignedRead.contigId], | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | store.readSeqStore[alignedRead.readId], alignedRead, errors, functor); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]' 250 | return value(me); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >]' 209 | if ((TVal1)*it1 == (TVal2)*it2) | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement, Alloc<> >, GapAnchor, void>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 529 | _alignAndGetCigarString(cigar, md, contigInfix, readSeq, alignedRead, errors, functor); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]' 905 | alignAndGetCigarString(record.cigar, record.qual, store.contigStore[alignedRead.contigId], | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | store.readSeqStore[alignedRead.readId], alignedRead, errors, functor); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >, GapsIterator > > > > > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >, GapsIterator > > > > > >]' 250 | return value(me); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >]' 209 | if ((TVal1)*it1 == (TVal2)*it2) | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:534:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement, Alloc<> >, GapAnchor, void>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 534 | _alignAndGetCigarString(cigar, md, contigInfix, reverseComplementString(readSeq), alignedRead, errors, functor); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]' 905 | alignAndGetCigarString(record.cigar, record.qual, store.contigStore[alignedRead.contigId], | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | store.readSeqStore[alignedRead.readId], alignedRead, errors, functor); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 520 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:663:20: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::end(ModifiedString&, Tag) [with THost = const Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]' 663 | TResult tmp(end(host(me), tag_)); | ~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:458:102: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]' 458 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); | ~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:811:66: required from 'void seqan::_fillBamSeqAndQual(TSeq&, TQual&, const TRead&) [with TSeq = String, Alloc<> >; TQual = String >; TRead = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]' 811 | typename Iterator::Type sIt = begin(read, Standard()); | ~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:936:31: required from 'void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]' 936 | _fillBamSeqAndQual(record.seq, record.qual, reverseComplementString(store.readSeqStore[alignedRead.readId])); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]' 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]' 174 | appendValue(me.strings, obj, tag); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]' 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:398:24: required from 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >]' 398 | appendValue(indexText(indexL), readSetL[j]); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = const Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]' 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = const Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]' 174 | appendValue(me.strings, obj, tag); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]' 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:859:24: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >]' 859 | appendValue(indexText(index), store.readSeqStore[j]); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]' 205 | return TProxy(it); | ^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]' 250 | return value(me); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:24: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >]' 209 | if ((TVal1)*it1 == (TVal2)*it2) | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]' 205 | return TProxy(it); | ^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]' 250 | return value(me); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >]' 209 | if ((TVal1)*it1 == (TVal2)*it2) | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >, GapsIterator > > > > > >]' 205 | return TProxy(it); | ^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >, GapsIterator > > > > > >]' 250 | return value(me); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >]' 209 | if ((TVal1)*it1 == (TVal2)*it2) | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]' 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:534:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:654:36: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 654 | TReadSet & readSetL = host(host(filterPatternL)); | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 512 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:469:24: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]' 469 | TIterator temp_(end(host(me), Rooted())); | ~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]' 301 | : data_iterator(begin(haystack, Rooted())) | ~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2241:41: required from 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]' 2241 | TMyersFinderRev myersFinderRev(infRev); | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Pigeonhole; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2795:64: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]' 2795 | std::cout << " stepsize: " << getStepSize(host(filterPattern)) << std::endl; | ~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1088:24: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:852:30: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >]' 852 | TIndex & index = host(tls.filterPattern); | ~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Pigeonhole; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:852:30: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]' 852 | TIndex & index = host(tls.filterPattern); | ~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:654:36: required from 'void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 654 | TReadSet & readSetL = host(host(filterPatternL)); | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:852:30: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]' 852 | TIndex & index = host(tls.filterPattern); | ~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:29: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:989:66: required from 'bool seqan::_patternInitSmallStateBanded(TFinder&, const TNeedle2&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = const Segment, Alloc<> >, InfixSegment>; TNeedle2 = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]' 989 | typename Size::Type const columns = length(container(finder)) + state.leftClip; | ~~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1181:44: required from 'bool seqan::_stateInit(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = const Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]' 1181 | return _patternInitSmallStateBanded(finder, needle, state); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1535:24: required from 'bool seqan::find(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = const Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]' 1535 | if (!_stateInit(finder, needle, state)) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1646:16: required from 'bool seqan::find(TFinder&, const TNeedle&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = const Segment, Alloc<> >, InfixSegment>; TSpec = AlignTextBanded; TFindBeginPatternSpec = void]' 1646 | return find(finder, needle, state); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2177:16: required from 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]' 2177 | while (find(myersFinder, readPrefix, state, minScore)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:61: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_interface.h:430:24: required from 'void seqan::goEnd(TIterator&) [with TIterator = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]' 430 | goEnd(it, container(it)); | ~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:737:10: required from 'void seqan::goEnd(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void]' 737 | goEnd(hostIterator(me)); | ~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1537:18: required from 'bool seqan::find(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]' 1537 | goEnd(finder); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1646:16: required from 'bool seqan::find(TFinder&, const TNeedle&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = AlignTextBanded; TFindBeginPatternSpec = void]' 1646 | return find(finder, needle, state); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2245:32: required from 'bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]' 2245 | while (find(myersFinderRev, readRev, verifier.revPatternState, maxScore)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2948:40: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 2948 | TReadSet & readSet = indexText(host(filterPattern)); | ~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Pigeonhole; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2795:64: required from 'void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]' 2795 | std::cout << " stepsize: " << getStepSize(host(filterPattern)) << std::endl; | ~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3026:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:41: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]' 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]' 174 | appendValue(me.strings, obj, tag); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]' 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:398:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]' 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]' 174 | appendValue(me.strings, obj, tag); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]' 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:398:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Pigeonhole >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)' first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = const Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = const Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]' 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = const Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]' 174 | appendValue(me.strings, obj, tag); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]' 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:859:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = const Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = const Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]' 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = const Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]' 174 | appendValue(me.strings, obj, tag); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]' 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:859:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 251 | limitRead(value(filter.callback), readId, newLimit - 1); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 466 | disabled += processRead(*tls.matchFilter, it->readId); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)' first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]' 339 | return value(me.data_host); | ~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2948:40: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]' 2948 | TReadSet & readSet = indexText(host(filterPattern)); | ~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3343 | return _mapSingleReads(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Swift > > >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)' first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 251 | limitRead(value(filter.callback), readId, newLimit - 1); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 466 | disabled += processRead(*tls.matchFilter, it->readId); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)' first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Pigeonhole >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)' first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 251 | limitRead(value(filter.callback), readId, newLimit - 1); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 466 | disabled += processRead(*tls.matchFilter, it->readId); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)' first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Swift > > >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)' first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 251 | limitRead(value(filter.callback), readId, newLimit - 1); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 466 | disabled += processRead(*tls.matchFilter, it->readId); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)' first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Pigeonhole >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 251 | limitRead(value(filter.callback), readId, newLimit - 1); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 466 | disabled += processRead(*tls.matchFilter, it->readId); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Swift > > >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 251 | limitRead(value(filter.callback), readId, newLimit - 1); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 466 | disabled += processRead(*tls.matchFilter, it->readId); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Pigeonhole >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 251 | limitRead(value(filter.callback), readId, newLimit - 1); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 466 | disabled += processRead(*tls.matchFilter, it->readId); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Swift > > >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 251 | limitRead(value(filter.callback), readId, newLimit - 1); | ~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]' 466 | disabled += processRead(*tls.matchFilter, it->readId); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]' 887 | create(me, value_); | ~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 135 | assignValue(*this, value_); | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:175:9: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:56: required from 'typename seqan::Source > > >::Type seqan::source(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 169 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 193 | else return *source(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const Proxy >&) [with TIterator = Iter, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > >; typename GetValue > >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 275 | return getValue(iter(me)); | ~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_base.h:151:37: required from 'typename seqan::Convert >::Type seqan::convertImpl(Convert, const Proxy&) [with TTarget = char; T = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; TSpec = IteratorProxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > >; typename Convert >::Type = char]' 151 | return convert(getValue(source)); | ~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_conversion.h:149:23: required from 'typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = char; TSource = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; typename Convert::Type = char]' 149 | return convertImpl(Convert(), source); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:241:45: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]' 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: required from 'TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]' 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag; TIntegral = long int]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:634:69: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]' 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: required from 'TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]' 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:46: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) | ~~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]' 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: required from 'TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]' 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:744:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 744 | TConstSeqHIterator seqHIter = seqHIterBegin; | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]' 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: required from 'TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]' 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 548 | valueConstruct(ret, data); | ~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 650 | me.data_value = _holderAllocateObject(me, value_); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 594 | create(me, _dataValue(me)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]' 863 | create(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:56: required from 'typename seqan::Source > > >::Type seqan::source(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 169 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 193 | else return *source(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const Proxy >&) [with TIterator = Iter, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > >; typename GetValue > >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 275 | return getValue(iter(me)); | ~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_alphabet_expansion.h:357:37: required from 'typename seqan::Convert >, seqan::Proxy >::Type seqan::convertImpl(Convert >, T>, const Proxy&) [with THost = SimpleType; char CHAR = '-'; TSpec = Tag; T = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; TSpec2 = IteratorProxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > >; typename Convert >, Proxy >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 357 | return convert(getValue(source_)); | ~~~~~~~~^~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_conversion.h:149:23: required from 'typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = ModifiedAlphabet, ModExpand<'-'> >; TSource = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; typename Convert::Type = ModifiedAlphabet, ModExpand<'-'> >]' 149 | return convertImpl(Convert(), source); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_alphabet_expansion.h:92:59: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 385 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:17: required from 'typename seqan::Source > > >::Type seqan::source(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 169 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 193 | else return *source(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const Proxy >&) [with TIterator = Iter, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > >; typename GetValue > >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 275 | return getValue(iter(me)); | ~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_base.h:151:37: required from 'typename seqan::Convert >::Type seqan::convertImpl(Convert, const Proxy&) [with TTarget = char; T = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; TSpec = IteratorProxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > >; typename Convert >::Type = char]' 151 | return convert(getValue(source)); | ~~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_conversion.h:149:23: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:994:55: required from 'void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag]' 994 | TConstSeqVIterator itVEnd = begin(seqV, Rooted()) + _min(seqVlength - 1, lowerDiagonal(band) + seqHlength); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:612:32: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 612 | _computeHammingDistance(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoringScheme, band, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 613 | dpProfile); | ~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]' 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:45: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]' 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 520 | return _endDefault(me, tag_); | ~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:29: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) | ~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]' 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(const ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = ModView > >; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:314:32: required from 'typename seqan::Position > >::Type seqan::position(const ModifiedIterator >&) [with THost = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >; typename Position > >::Type = long unsigned int]' 314 | return length(container(host(me))); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:675:73: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 675 | sequenceEntryForScore(scoringScheme, seqV, position(seqVBegin)), scoringScheme, | ~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]' 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:288:16: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 288 | TContainer cont(container(host(me))); | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 2%] Linking CXX executable ../../bin/rabema_build_gold_standard cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_build_gold_standard.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic -Wl,--dependency-file=CMakeFiles/rabema_build_gold_standard.dir/link.d CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -o ../../bin/rabema_build_gold_standard -lrt -lz -lbz2 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Built target rabema_build_gold_standard make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/sak /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/sak/CMakeFiles/sak.dir/sak.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/sak && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.4.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/sak/CMakeFiles/sak.dir/sak.cpp.o -MF CMakeFiles/sak.dir/sak.cpp.o.d -o CMakeFiles/sak.dir/sak.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | : data_container(_toPointer(container_)), | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: required from 'seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]' 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:56: required from 'typename seqan::Source > > >::Type seqan::source(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 169 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 193 | else return *source(me); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const Proxy >&) [with TIterator = Iter, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > >; typename GetValue > >::Type = ModifiedAlphabet, ModExpand<'-'> >]' 275 | return getValue(iter(me)); | ~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_base.h:151:37: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1210 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = ModView > >; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:30: required from 'typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]' 278 | TContainer cont(container(host(me))); | ~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:397:81: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSeqHValue = SimpleType; TSeqVValue = SimpleType; TSeqVIterator = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >; TScoringScheme = Score >; TDPCell = DPCell_ >; TColumnDescriptor = MetaColumnDescriptor, Tag >; TDPProfile = DPProfile_ >, Tag, TracebackOn, Tag > >, Tag >]' 397 | tmpSeqH, sequenceEntryForScore(scoringScheme, container(iter), position(iter)), | ~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:891:38: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]' 891 | _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 892 | sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 893 | sequenceEntryForScore(scoringScheme, seqV, 0), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 894 | seqVBegin, seqVEnd, scoringScheme, cacheDiag, cacheVert, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 895 | MetaColumnDescriptor(), dpProfile); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]' 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]' 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); | ~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]' 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]' 1215 | writeAlignments(bamFile, store, func); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]' 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]' 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 257 | dumpMatches(store, stats, readFileNames[0], options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; TSource = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:702:11: required from 'void seqan::assignValue(T&, TPos, const TValue&) [with T = String, AlignedReadStoreElement, void>, long unsigned int>, Alloc<> >; TValue = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; TPos = unsigned int]' 702 | assign(value(me, pos), _value); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_types/property_map_generic.h:186:16: required from 'typename seqan::EnableIf >, void>::Type seqan::assignProperty(TPropertyMap&, TDescriptor, TValue) [with TPropertyMap = String, AlignedReadStoreElement, void>, long unsigned int>, Alloc<> >; TDescriptor = unsigned int; TValue = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; typename EnableIf >, void>::Type = void]' 186 | assignValue(pm, _getId(d), val); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph_base.h:191:23: required from 'GraphCargo& registerRead(ReadGraph&, typename ReadGraph::TId) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int; typename ReadGraph::TId = unsigned int]' 191 | assignProperty(me.vertexCargo, vd, new_cargo); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph_construction.h:82:59: required from 'void construct(ReadGraph&, const seqan::String > >&, const seqan::FragmentStore&, TId) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int; TSpec = void; TConfig = seqan::FragmentStoreConfig; TId = int]' 82 | TGraphCargo & new_cargo = registerRead(me, _readId(value(colIter))); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:217:14: required from here 217 | construct(rgraph, candidates, fragStore, options.contig); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>& GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>::operator=(const GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>&)' is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph.h:32, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:34: /build/reproducible-path/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph_base.h:44:5: note: because 'GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>' has user-provided 'GraphCargo::GraphCargo(const GraphCargo&) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int]' 44 | GraphCargo(GraphCargo const& other) | ^~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 889 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 924 | assignValue(target_, value(source_)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' 150 | assign(*this, source_); | ~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]' 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 889 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 924 | assignValue(target_, value(source_)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' 150 | assign(*this, source_); | ~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]' 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 889 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]' 924 | assignValue(target_, value(source_)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' 150 | assign(*this, source_); | ~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]' 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 889 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]' 924 | assignValue(target_, value(source_)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' 150 | assign(*this, source_); | ~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]' 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 889 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 924 | assignValue(target_, value(source_)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' 150 | assign(*this, source_); | ~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]' 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 889 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]' 924 | assignValue(target_, value(source_)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' 150 | assign(*this, source_); | ~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]' 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 645 | assign(_dataValue(me), value_); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3422 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' 143 | Index(Index const &other): | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3431 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3443 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3376 | return _mapReads(store, cnts, options, ungapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 305 | TConstructor::construct(it, std::forward(param_)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*]' 511 | valueConstruct(target_begin, std::move(*source_begin)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]' 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]' 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]' 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]' 3381 | return _mapReads(store, cnts, options, gapped, mode); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]' 3396 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]' 3452 | return _mapReads(store, cnts, options, RazerSMode()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:26: required from here 866 | int result = mapReads(genomeFileNames, readFileNames, options); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Built target pair_align_global_0100 make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/sam2matrix /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/sam2matrix/CMakeFiles/sam2matrix.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/sam2matrix && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -MF CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o.d -o CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:46: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:55: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short unsigned int; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = signed char; TSource = char*]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = char*]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = signed char]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:620:16, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, char*>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:151:30: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const signed char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = signed char; TSource = char*]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short int; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = short int; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = unsigned char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:627:13, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = signed char; TSource = String >]', inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from 'bool seqan::AppendTagsSamToBamOneTagHelper_::operator()(Type) [with Type = signed char; TTarget = seqan::String >; TBuffer = seqan::String >&]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = signed char]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:620:16, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned char; TSubList = TagList]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = char; TSubList = TagList >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short unsigned int; TSubList = TagList > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = short int; TSubList = TagList > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = float; TSubList = TagList > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = unsigned int; TSubList = TagList > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'bool seqan::tagApply(TFunctor&, TagList) [with TFunctor = AppendTagsSamToBamOneTagHelper_ >, String >&>; TTag = int; TSubList = TagList > > > > > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_tags.h:629:20, inlined from 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:166:26: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::_appendTagsSamToBamOneTag(TTarget&, TForwardIter&, CharString&) [with TTarget = String >; TForwardIter = Iter >, AdaptorIterator > >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const signed char&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = signed char; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]', inlined from 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_sam.h:320:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = String >]', inlined from 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]' at /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_sam.h:363:43: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(BamAlignmentRecord&, BamIOContext&, TForwardIter&, const Sam&) [with TForwardIter = Iter >, StreamIterator > >; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:46: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:221:39: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:60, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:73: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:352:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:362:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:372:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:382:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:392:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_align.h:402:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2155:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:337:23: required from here 337 | openRes = open(inFile, toCString(options.inFastxPath)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:337:23: required from here 337 | openRes = open(inFile, toCString(options.inFastxPath)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:337:23: required from here 337 | openRes = open(inFile, toCString(options.inFastxPath)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:347:23: required from here 347 | openRes = open(outFile, toCString(options.outPath)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:337:23: required from here 337 | openRes = open(inFile, toCString(options.inFastxPath)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TSequence = Segment, Alloc<> >, InfixSegment>; TSize = int]' 489 | TIter iter = begin(seq, Rooted()); | ~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:468:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf, Tag > > >, void>::Type = void; Fastq = Tag]' 468 | writeWrappedString(target, seq, lineLength); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const Tag&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TagSpec = TagFastq_]' 423 | writeRecord(file.iter, meta, seq, qual, Tag(), context(file).options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const TagSelector&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]' 506 | writeRecord(file, meta, seq, qual, TFormat()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = FormattedFile, Tag >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf >, IsSequence >, void>::Type = void; typename TFile::TStream = VirtualStream, std::char_traits >]' 519 | writeRecord(file, meta, seq, qual, file.format); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:24: required from here 424 | writeRecord(outFile, id, infix(seqCopy, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TSequence = Segment >, InfixSegment>; TSize = int]' 489 | TIter iter = begin(seq, Rooted()); | ~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:475:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf, Tag > > >, void>::Type = void; Fastq = Tag]' 475 | writeWrappedString(target, qual, lineLength); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const Tag&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TagSpec = TagFastq_]' 423 | writeRecord(file.iter, meta, seq, qual, Tag(), context(file).options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const TagSelector&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]' 506 | writeRecord(file, meta, seq, qual, TFormat()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = FormattedFile, Tag >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf >, IsSequence >, void>::Type = void; typename TFile::TStream = VirtualStream, std::char_traits >]' 519 | writeRecord(file, meta, seq, qual, file.format); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:24: required from here 424 | writeRecord(outFile, id, infix(seqCopy, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | : data_container(_toPointer(container_)), | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]' 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TSequence = Segment, Alloc<> >, InfixSegment>; TSize = int]' 489 | TIter iter = begin(seq, Rooted()); | ~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:468:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf, Tag > > >, void>::Type = void; Fastq = Tag]' 468 | writeWrappedString(target, seq, lineLength); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const Tag&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TagSpec = TagFastq_]' 423 | writeRecord(file.iter, meta, seq, qual, Tag(), context(file).options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const TagSelector&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]' 506 | writeRecord(file, meta, seq, qual, TFormat()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = FormattedFile, Tag >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf >, IsSequence >, void>::Type = void; typename TFile::TStream = VirtualStream, std::char_traits >]' 519 | writeRecord(file, meta, seq, qual, file.format); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:24: required from here 424 | writeRecord(outFile, id, infix(seqCopy, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 117 | : data_container(_toPointer(container_)), | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]' 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TSequence = Segment >, InfixSegment>; TSize = int]' 489 | TIter iter = begin(seq, Rooted()); | ~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:475:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf, Tag > > >, void>::Type = void; Fastq = Tag]' 475 | writeWrappedString(target, qual, lineLength); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const Tag&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TagSpec = TagFastq_]' 423 | writeRecord(file.iter, meta, seq, qual, Tag(), context(file).options); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const TagSelector&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]' 506 | writeRecord(file, meta, seq, qual, TFormat()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = FormattedFile, Tag >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf >, IsSequence >, void>::Type = void; typename TFile::TStream = VirtualStream, std::char_traits >]' 519 | writeRecord(file, meta, seq, qual, file.format); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:24: required from here 424 | writeRecord(outFile, id, infix(seqCopy, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' 257 | _open(*this, fileName, openMode, True()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' 257 | _open(*this, fileName, openMode, True()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' 257 | _open(*this, fileName, openMode, True()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' 257 | _open(*this, fileName, openMode, True()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]' /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' 257 | _open(*this, fileName, openMode, True()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); | ^ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Built target pair_align_global_0000 make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/samcat /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/samcat /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/samcat/CMakeFiles/samcat.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/samcat && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o -MF CMakeFiles/samcat.dir/samcat.cpp.o.d -o CMakeFiles/samcat.dir/samcat.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = Segment >, PrefixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::Segment >, seqan::PrefixSegment>]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = Segment >, SuffixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::Segment >, seqan::SuffixSegment>]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = long int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const long int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = long int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = long int; TSource = Segment >, PrefixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const long int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = long int; TSource = seqan::Segment >, seqan::PrefixSegment>]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = long int; TSource = Segment >, SuffixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const long int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = long int; TSource = seqan::Segment >, seqan::SuffixSegment>]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:37: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:35: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align.h:88: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:224:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/align/gap_anchor.h:234:17: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 2%] Linking CXX executable ../../bin/rabema_evaluate cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_evaluate.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic -Wl,--dependency-file=CMakeFiles/rabema_evaluate.dir/link.d CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -o ../../bin/rabema_evaluate -lrt -lz -lbz2 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Built target rabema_evaluate make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/searchjoin /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/searchjoin/CMakeFiles/s4_search.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/searchjoin/CMakeFiles/s4_search.dir/search.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/searchjoin && /usr/bin/c++ -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/searchjoin/CMakeFiles/s4_search.dir/search.cpp.o -MF CMakeFiles/s4_search.dir/search.cpp.o.d -o CMakeFiles/s4_search.dir/search.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp [ 2%] Linking CXX executable ../../bin/razers3_simulate_reads cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3_simulate_reads.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic -Wl,--dependency-file=CMakeFiles/razers3_simulate_reads.dir/link.d CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -o ../../bin/razers3_simulate_reads -lrt -lz -lbz2 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Built target razers3_simulate_reads make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/searchjoin /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/searchjoin/CMakeFiles/s4_join.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/searchjoin && /usr/bin/c++ -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o -MF CMakeFiles/s4_join.dir/join.cpp.o.d -o CMakeFiles/s4_join.dir/join.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/parallel/base.h:36, from /usr/include/c++/14/parallel/algobase.h:40, from /usr/include/c++/14/parallel/algorithm:36, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:48: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:36: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:58: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/parallel/base.h:36, from /usr/include/c++/14/parallel/algobase.h:40, from /usr/include/c++/14/parallel/algorithm:36, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:48: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 151 | _host(_toPointer(host)), tmp_value() | ~~~~~~~~~~^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]' 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]' 114 | if (guessFormatFromFilename(fname, TFormat())) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]' 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]' 739 | return _open(file, fileName, openMode, False()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:14: required from here 699 | if (!open(bamFile, bamFilename)) | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ [ 2%] Linking CXX executable ../../bin/razers3_quality2prob cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3_quality2prob.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic -Wl,--dependency-file=CMakeFiles/razers3_quality2prob.dir/link.d CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -o ../../bin/razers3_quality2prob -lrt -lz -lbz2 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Built target razers3_quality2prob make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/seqan2-2.4.0+dfsg /build/reproducible-path/seqan2-2.4.0+dfsg/apps/seqan_tcoffee /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/seqan_tcoffee /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build make[4]: Entering directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' [ 2%] Building CXX object apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/seqan_tcoffee && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.13.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -MF CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o.d -o CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:45:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:54:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_filter.h:63:35: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:46: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:351:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:457:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe.h:78: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:42:46: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:57:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:206:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_sorter.h:321:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:48, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find.h:47, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:46: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms.h:62: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_algorithms/kruskal.h:63:34: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:47: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/misc/set.h:373:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:76: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:340:35: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:646:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:660:68: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:91: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:666:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:714:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:782:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:851:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:885:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:933:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1814:33: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1833:13: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:102: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:46:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_qsort.h:85:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:107: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:98:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:112:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:127:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:144:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:154:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:110: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:110:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:143:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:111: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:65:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:99:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:118:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:132:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:154:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:175:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:185:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:114: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:57:43: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:97:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:141:21: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:121: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:59:38: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_lcp.h:164:43: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:125: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_bwt.h:144:44: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:131: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:556:21: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:74, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:79:36: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:22: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:113:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:147:37: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:219:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:228:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:237:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:246:45: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:255:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:264:46: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:276:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:287:47: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:188: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/repeat_base.h:120:38: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier.h:79: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:393:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file.h:92: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1338:41: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream.h:119: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = short unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const short unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = short unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ c++: fatal error: Killed signal terminated program cc1plus compilation terminated. make[4]: *** [apps/razers3/CMakeFiles/razers3.dir/build.make:82: apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o] Error 1 make[4]: Leaving directory '/build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:21268: apps/razers3/CMakeFiles/razers3.dir/all] Error 2 make[3]: *** Waiting for unfinished jobs.... [ 2%] Building CXX object apps/razers/CMakeFiles/razers.dir/param_tabs.cpp.o cd /build/reproducible-path/seqan2-2.4.0+dfsg/obj-aarch64-linux-gnu/apps/razers && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/reproducible-path/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers/CMakeFiles/razers.dir/param_tabs.cpp.o -MF CMakeFiles/razers.dir/param_tabs.cpp.o.d -o CMakeFiles/razers.dir/param_tabs.cpp.o -c /build/reproducible-path/seqan2-2.4.0+dfsg/apps/razers/param_tabs.cpp /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:355:10: required from 'void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 355 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 264 | index(joiner); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:319:37: required from here 319 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Exact()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:142: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 264 | index(joiner); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:41: required from here 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:279:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 279 | prepare(joiner, db); | ~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:41: required from here 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:355:10: required from 'void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 355 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 264 | index(joiner); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:332:37: required from here 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Exact()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 264 | index(joiner); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:41: required from here 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:279:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 279 | prepare(joiner, db); | ~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:41: required from here 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:355:10: required from 'void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 355 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 264 | index(joiner); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:357:37: required from here 357 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Exact()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 264 | index(joiner); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:41: required from here 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:279:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 279 | prepare(joiner, db); | ~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:41: required from here 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:355:10: required from 'void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 355 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 264 | index(joiner); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:370:37: required from here 370 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Exact()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 264 | index(joiner); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:41: required from here 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:279:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 279 | prepare(joiner, db); | ~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:41: required from here 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:138: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 311 | _historyClear(it); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:41: required from here 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 311 | _historyClear(it); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:41: required from here 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 311 | _historyClear(it); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:41: required from here 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 311 | _historyClear(it); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:41: required from here 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]' 2236 | _clear(it); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 312 | clear(it); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:41: required from here 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]' 2236 | _clear(it); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 312 | clear(it); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:41: required from here 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]' 2236 | _clear(it); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 312 | clear(it); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:41: required from here 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]' 2236 | _clear(it); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 312 | clear(it); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:41: required from here 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]' 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' 78 | return _verify(*this, dbId, queryId, delegate); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 791 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:29: required from here 311 | return runJoiner(options, TDbDna(), Nothing(), Online()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]' 515 | return begin(cont, Rooted()); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter, StreamIterator > >; TContainer = Segment >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = char]' 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:132:10: required from 'void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]' 132 | write(writer.outputIt, id1); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:197:21: required from 'bool close(Writer >&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>]' 197 | _writeRecord(writer, writer.db.ids[dbId], writer.db.ids[dbId]); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:293:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' 293 | close(writer); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:29: required from here 311 | return runJoiner(options, TDbDna(), Nothing(), Online()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter > >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]' 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' 78 | return _verify(*this, dbId, queryId, delegate); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 791 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:349:29: required from here 349 | return runJoiner(options, TDbGeo(), Nothing(), Online()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]' 377 | _historyPush(it); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]' 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 432 | if (_moveIteratorsDown(finder, TStage())) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]' 1311 | if (_pushState(finder, TStage())) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 611 | _find(finderExt, dbFinder, StageInitial_()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:41: required from here 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]' 377 | _historyPush(it); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Truncated]' 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 432 | if (_moveIteratorsDown(finder, TStage())) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]' 1311 | if (_pushState(finder, TStage())) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 611 | _find(finderExt, dbFinder, StageInitial_()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:41: required from here 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]' 377 | _historyPush(it); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]' 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 432 | if (_moveIteratorsDown(finder, TStage())) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]' 1311 | if (_pushState(finder, TStage())) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 611 | _find(finderExt, dbFinder, StageInitial_()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:41: required from here 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]' 377 | _historyPush(it); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Truncated]' 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 432 | if (_moveIteratorsDown(finder, TStage())) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]' 1311 | if (_pushState(finder, TStage())) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 611 | _find(finderExt, dbFinder, StageInitial_()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:41: required from here 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]' 377 | _historyPush(it); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]' 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 432 | if (_moveIteratorsDown(finder, TStage())) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]' 1311 | if (_pushState(finder, TStage())) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 611 | _find(finderExt, dbFinder, StageInitial_()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:41: required from here 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]' 377 | _historyPush(it); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Truncated]' 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 432 | if (_moveIteratorsDown(finder, TStage())) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]' 1311 | if (_pushState(finder, TStage())) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 611 | _find(finderExt, dbFinder, StageInitial_()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:41: required from here 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]' 377 | _historyPush(it); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]' 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 432 | if (_moveIteratorsDown(finder, TStage())) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]' 1311 | if (_pushState(finder, TStage())) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 611 | _find(finderExt, dbFinder, StageInitial_()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:41: required from here 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]' 377 | _historyPush(it); | ~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Truncated]' 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]' 432 | if (_moveIteratorsDown(finder, TStage())) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]' 1311 | if (_pushState(finder, TStage())) | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 611 | _find(finderExt, dbFinder, StageInitial_()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:41: required from here 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc > >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' 117 | : data_container(_toPointer(container_)), | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]' 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]' 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' 78 | return _verify(*this, dbId, queryId, delegate); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' 791 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:29: required from here 311 | return runJoiner(options, TDbDna(), Nothing(), Online()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 117 | : data_container(_toPointer(container_)), | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]' 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]' 515 | return begin(cont, Rooted()); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter, StreamIterator > >; TContainer = Segment >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = char]' 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:132:10: required from 'void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]' 132 | write(writer.outputIt, id1); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:197:21: required from 'bool close(Writer >&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>]' 197 | _writeRecord(writer, writer.db.ids[dbId], writer.db.ids[dbId]); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:293:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' 293 | close(writer); | ~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:29: required from here 311 | return runJoiner(options, TDbDna(), Nothing(), Online()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment > >, InfixSegment>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]' 117 | : data_container(_toPointer(container_)), | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]' 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter > >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >]' 392 | return _beginDefault(me, tag_); | ~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]' 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); | ~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' 78 | return _verify(*this, dbId, queryId, delegate); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' 791 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' 286 | execute(joiner); | ~~~~~~~^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:349:29: required from here 349 | return runJoiner(options, TDbGeo(), Nothing(), Online()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]' 143 | operator = (Segment const & source) | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:282:10: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' 282 | index(searcher); | ~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:39: required from here 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:142: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:323:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' 323 | prepare(searcher, query); | ~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:39: required from here 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:282:10: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' 282 | index(searcher); | ~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:39: required from here 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:323:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' 323 | prepare(searcher, query); | ~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:39: required from here 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:405:10: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' 405 | index(searcher); | ~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:39: required from here 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:449:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' 449 | prepare(searcher, queryLong); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:39: required from here 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:405:10: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' 405 | index(searcher); | ~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:39: required from here 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]': /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:449:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' 449 | prepare(searcher, queryLong); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:39: required from here 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' 88 | Index(Index const & other) : | ^~~~~ In file included from /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index.h:138: /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 311 | _historyClear(it); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' 330 | execute(searcher); | ~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:39: required from here 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 311 | _historyClear(it); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' 330 | execute(searcher); | ~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:39: required from here 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 311 | _historyClear(it); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' 456 | execute(searcher); | ~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:39: required from here 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 311 | _historyClear(it); | ~~~~~~~~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' 456 | execute(searcher); | ~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:39: required from here 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]': /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]' 2236 | _clear(it); | ~~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]' 312 | clear(it); | ~~~~~^~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' 212 | goRoot(*this); | ~~~~~~^~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' 605 | TTextIterator textIt(dbFinder.dbIndex.index); | ^~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' 330 | execute(searcher); | ~~~~~~~^~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:39: required from here 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ make[4]: *** Deleting file 'apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o' make[4]: *** [apps/searchjoin/CMakeFiles/s4_join.dir/build.make:82: apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o] Terminated make[4]: *** wait: No child processes. Stop. make[4]: *** Waiting for unfinished jobs.... make[4]: *** wait: No child processes. Stop. make[4]: *** [apps/samcat/CMakeFiles/samcat.dir/build.make:82: apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o] Terminated make[4]: *** [apps/searchjoin/CMakeFiles/s4_search.dir/build.make:82: apps/searchjoin/CMakeFiles/s4_search.dir/search.cpp.o] Terminated make[4]: *** wait: No child processes. Stop. make[4]: *** Waiting for unfinished jobs.... make[4]: *** wait: No child processes. Stop. make[3]: *** [CMakeFiles/Makefile2:21556: apps/searchjoin/CMakeFiles/s4_join.dir/all] Terminated make[3]: *** [CMakeFiles/Makefile2:21460: apps/sam2matrix/CMakeFiles/sam2matrix.dir/all] Error 2 make[3]: *** [CMakeFiles/Makefile2:21492: apps/samcat/CMakeFiles/samcat.dir/all] Terminated make[3]: *** [CMakeFiles/Makefile2:21524: apps/searchjoin/CMakeFiles/s4_search.dir/all] Terminated make[4]: *** [apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make:82: apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o] Terminated make[3]: *** [CMakeFiles/Makefile2:21588: apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/all] Terminated make[3]: *** [CMakeFiles/Makefile2:21396: apps/sak/CMakeFiles/sak.dir/all] Error 2 make[4]: *** [apps/rep_sep/CMakeFiles/rep_sep.dir/build.make:82: apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o] Terminated make[3]: *** [CMakeFiles/Makefile2:21364: apps/rep_sep/CMakeFiles/rep_sep.dir/all] Terminated make[4]: *** [apps/razers/CMakeFiles/razers.dir/build.make:82: apps/razers/CMakeFiles/razers.dir/razers.cpp.o] Terminated make[4]: *** [apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make:82: apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o] Terminated make[1]: *** [debian/rules:76: override_dh_auto_build-arch] Terminated make[4]: *** [apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make:82: apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o] Terminated make[2]: *** [Makefile:149: all] Terminated Terminated make[4]: *** [apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make:82: apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o] Terminated make: *** [debian/rules:45: binary] Terminated I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem W: Stray processes left from build: * system-pbuilder-build-seqan2_2.4.0\x2bdfsg\x2d16-995300.slice - Slice /system/pbuilder/build/seqan2_2.4.0+dfsg-16/995300 Loaded: loaded Active: active since Thu 2025-06-05 18:42:22 -12; 10min ago Tasks: 3 Memory: 1.6G CPU: 35min 36.774s CGroup: /system.slice/system-pbuilder.slice/system-pbuilder-build.slice/system-pbuilder-build-seqan2_2.4.0\x2bdfsg\x2d16.slice/system-pbuilder-build-seqan2_2.4.0\x2bdfsg\x2d16-995300.slice `-run-r8298d124f8bf42ebab0552b688b85369.scope |-1004463 /usr/libexec/gcc/aarch64-linux-gnu/14/cc1plus -quiet -I /build/reproducible-path/seqan2-2.4.0+dfsg/include -imultiarch aarch64-linux-gnu -MD CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.d -MF CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o.d -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o -D_GNU_SOURCE -D_REENTRANT -D "SEQAN_APP_VERSION=\"1.3.8\"" -D "SEQAN_DATE=\"\"" -D SEQAN_DISABLE_VERSION_CHECK -D SEQAN_HAS_BZIP2=1 -D SEQAN_HAS_EXECINFO=1 -D SEQAN_HAS_OPENMP=1 -D SEQAN_HAS_ZLIB=1 -D "SEQAN_REVISION=\"tarball\"" -D SUFFIX_GAP_BOTTOM=0 -D SUFFIX_GAP_LEFT=1 -D SUFFIX_GAP_RIGHT=1 -D SUFFIX_GAP_TOP=0 -D _FILE_OFFSET_BITS=64 -D _LARGEFILE_SOURCE -D NDEBUG -D _FORTIFY_SOURCE=2 -D SEQAN_GLOBAL_EXCEPTION_HANDLER=1 /build/reproducible-path/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp -quiet -dumpdir CMakeFiles/pair_align_global_0110.dir/ -dumpbase pair_align_global.cpp.cpp -dumpbase-ext .cpp -mbranch-protection=standard -mlittle-endian -mabi=lp64 -g -O2 -O3 -Wformat=1 -Werror=format-security -Wdate-time -Wextra -Wall -Wpedantic -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -fopenmp -fasynchronous-unwind-tables -o /tmp/ccDJyp0C.s |-1017679 /usr/libexec/gcc/aarch64-linux-gnu/14/cc1plus -quiet -I /build/reproducible-path/seqan2-2.4.0+dfsg/include -imultiarch aarch64-linux-gnu -MD CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.d -MF CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o.d -MT apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -D_GNU_SOURCE -D_REENTRANT -D "SEQAN_APP_VERSION=\"1.13.8\"" -D "SEQAN_DATE=\"\"" -D SEQAN_DISABLE_VERSION_CHECK -D SEQAN_HAS_BZIP2=1 -D SEQAN_HAS_EXECINFO=1 -D SEQAN_HAS_OPENMP=1 -D SEQAN_HAS_ZLIB=1 -D "SEQAN_REVISION=\"tarball\"" -D _FILE_OFFSET_BITS=64 -D _LARGEFILE_SOURCE -D NDEBUG -D _FORTIFY_SOURCE=2 -D SEQAN_GLOBAL_EXCEPTION_HANDLER=1 /build/reproducible-path/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp -quiet -dumpdir CMakeFiles/seqan_tcoffee.dir/ -dumpbase seqan_tcoffee.cpp.cpp -dumpbase-ext .cpp -mbranch-protection=standard -mlittle-endian -mabi=lp64 -g -O2 -O3 -Wformat=1 -Werror=format-security -Wdate-time -Wextra -Wall -Wpedantic -fdebug-prefix-map=/build/reproducible-path/seqan2-2.4.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -fopenmp -fasynchronous-unwind-tables -o /tmp/ccCqTD7G.s `-1017771 as -I /build/reproducible-path/seqan2-2.4.0+dfsg/include --gdwarf-5 -EL -mabi=lp64 -o CMakeFiles/rep_sep.dir/rep_sep.cpp.o /tmp/ccwJxAWd.s Jun 05 18:42:22 codethink04-arm64 systemd[1]: Created slice system-pbuilder-build-seqan2_2.4.0\x2bdfsg\x2d16-995300.slice - Slice /system/pbuilder/build/seqan2_2.4.0+dfsg-16/995300. I: cleaning the build env I: removing directory /srv/workspace/pbuilder/995300 and its subdirectories seqan2 failed to build from source. removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/seqan2_2.4.0+dfsg-16.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/seqan2_2.4.0+dfsg-16.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/seqan2_2.4.0+dfsg-16.build1.log.gz' Fri Jun 6 06:53:20 UTC 2025 W: No second build log, what happened? Compressing the 1st log... b1/build.log: 95.9% -- replaced with stdout INSERT 0 1 INSERT 0 1 DELETE 1 [2025-06-06 06:53:21] INFO: Starting at 2025-06-06 06:53:21.266523 [2025-06-06 06:53:21] INFO: Generating the pages of 1 package(s) [2025-06-06 06:53:21] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/seqan2 didn't produce a buildlog, even though it has been built. [2025-06-06 06:53:21] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/experimental/arm64/seqan2_2.5.0~rc3+dfsg-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/arm64/seqan2_2.5.0~rc3+dfsg-1.diff.gz is missing [2025-06-06 06:53:21] INFO: Finished at 2025-06-06 06:53:21.607288, took: 0:00:00.340768 Fri Jun 6 06:53:21 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/seqan2.html Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/seqan2_2.4.0+dfsg-16.rbuild.log: 95.9% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/seqan2_2.4.0+dfsg-16.rbuild.log.gz [2025-06-06 06:53:21] INFO: Starting at 2025-06-06 06:53:21.958107 [2025-06-06 06:53:22] INFO: Generating the pages of 1 package(s) [2025-06-06 06:53:22] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/seqan2_2.4.0+dfsg-16.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/seqan2_2.4.0+dfsg-16.diff.gz is missing [2025-06-06 06:53:22] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/experimental/arm64/seqan2_2.5.0~rc3+dfsg-1.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/arm64/seqan2_2.5.0~rc3+dfsg-1.diff.gz is missing [2025-06-06 06:53:22] INFO: Finished at 2025-06-06 06:53:22.271214, took: 0:00:00.313110 All cleanup done. Fri Jun 6 06:53:22 UTC 2025 - total duration: 0h 11m 13s. Fri Jun 6 06:53:22 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-DaFIiwhu, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 11min 14.740s CPU time consumed: 4.289s